Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/69c7d2a4ae58ab92cf601e7b589836/tih_rna_sample_00570_B23MVV7LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/b8e0e405088870a69e794b1c02fefb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/69c7d2a4ae58ab92cf601e7b589836/tih_rna_sample_00570_B23MVV7LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/b8e0e405088870a69e794b1c02fefb/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/3e8b864b55a8710d5970c15b92bc8b/tih_rna_sample_00570_B23MVV7LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00570_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00570_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf > /tmp/nxf.8hThpsG6it/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf > /tmp/nxf.8hThpsG6it/cytoBand.txt
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.bed > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.bed > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00570_B23MVV7LT4_1.star --out_dir /tmp/nxf.8hThpsG6it/fi_workdir --reads "/tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.8hThpsG6it/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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:30:16 ..... started STAR run
Jun 08 10:30:16 ..... loading genome
Jun 08 10:32:01 ... generating Suffix Array index
Jun 08 10:35:54 ... completed Suffix Array index
Jun 08 10:35:54 ..... processing annotations GTF
Jun 08 10:35:54 ..... inserting junctions into the genome indices
Jun 08 10:36:56 ..... started mapping
Jun 08 11:59:26 ..... finished mapping
Jun 08 11:59:27 ..... started sorting BAM
Jun 08 11:59:28 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00570_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00570_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 89.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00570_B23MVV7LT4_1.star --out_dir /tmp/nxf.8hThpsG6it/fi_workdir --reads "/tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:59:36 : INFO : Done.
Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.8hThpsG6it/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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[1350000]   -done parsing /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num genes matched < 2' => 18,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 15,
          'excessive soft clipping' => 6732,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 87,
          'small anchor length' => 121,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 30,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3,
          'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 18,
          ' ** passed ** ' => 15988,
          'per_id < 96' => 4677,
          'seq-similar region overlap' => 156,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 105,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 11,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38
        };
-writing fusion junction support info.
Execution Time = 0.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.8hThpsG6it/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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
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[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
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[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
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[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

[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]   
[31000]   
[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: OTUD4--HERC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -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]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -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]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

[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: PCDHGA4--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5

[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]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12

[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: PCDHGA4--PCDHGA11

[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]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9

[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: PCDHGA5--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

[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: PCDHGA5--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

[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: PCDHGA5--PCDHGA11

[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]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

[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: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[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: PCDHGB2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[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: PCDHGB2--PCDHGA11

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[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]   -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]   
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[28000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[20000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 86520,
          'lacks exon overlap' => 39194
        };
Execution Time = 1.53 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.8hThpsG6it/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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4597.155498
EM: Round [1] log likelihood: -4596.123877
EM: Round [2] log likelihood: -4595.664037
EM: Round [3] log likelihood: -4595.256284
EM: Round [4] log likelihood: -4594.892964
EM: Round [5] log likelihood: -4594.568176
EM: Round [6] log likelihood: -4594.276920
EM: Round [7] log likelihood: -4594.014929
EM: Round [8] log likelihood: -4593.778556
EM: Round [9] log likelihood: -4593.564671
EM: Round [10] log likelihood: -4593.370581
EM: Round [11] log likelihood: -4593.193964
EM: Round [12] log likelihood: -4593.032811
EM: Round [13] log likelihood: -4592.885381
EM: Round [14] log likelihood: -4592.750162
EM: Round [15] log likelihood: -4592.625837
EM: Round [16] log likelihood: -4592.511257
EM: Round [17] log likelihood: -4592.405419
EM: Round [18] log likelihood: -4592.307440
EM: Round [19] log likelihood: -4592.216548
EM: Round [20] log likelihood: -4592.132060
EM: Round [21] log likelihood: -4592.053374
EM: Round [22] log likelihood: -4591.979958
EM: Round [23] log likelihood: -4591.911338
EM: Round [24] log likelihood: -4591.847093
EM: Round [25] log likelihood: -4591.786849
EM: Round [26] log likelihood: -4591.730270
EM: Round [27] log likelihood: -4591.677054
EM: Round [28] log likelihood: -4591.626931
EM: Round [29] log likelihood: -4591.579657
EM: Round [30] log likelihood: -4591.535012
EM: Round [31] log likelihood: -4591.492795
EM: Round [32] log likelihood: -4591.452827
EM: Round [33] log likelihood: -4591.414943
EM: Round [34] log likelihood: -4591.378991
EM: Round [35] log likelihood: -4591.344836
EM: Round [36] log likelihood: -4591.312351
EM: Round [37] log likelihood: -4591.281422
EM: Round [38] log likelihood: -4591.251943
EM: Round [39] log likelihood: -4591.223816
EM: Round [40] log likelihood: -4591.196953
EM: Round [41] log likelihood: -4591.171269
EM: Round [42] log likelihood: -4591.146690
EM: Round [43] log likelihood: -4591.123145
EM: Round [44] log likelihood: -4591.100567
EM: Round [45] log likelihood: -4591.078898
EM: Round [46] log likelihood: -4591.058079
EM: Round [47] log likelihood: -4591.038060
EM: Round [48] log likelihood: -4591.018792
EM: Round [49] log likelihood: -4591.000229
EM: Round [50] log likelihood: -4590.982330
EM: Round [51] log likelihood: -4590.965056
EM: Round [52] log likelihood: -4590.948370
EM: Round [53] log likelihood: -4590.932238
EM: Round [54] log likelihood: -4590.916629
EM: Round [55] log likelihood: -4590.901513
EM: Round [56] log likelihood: -4590.886863
EM: Round [57] log likelihood: -4590.872652
EM: Round [58] log likelihood: -4590.858857
EM: Round [59] log likelihood: -4590.845455
EM: Round [60] log likelihood: -4590.832426
EM: Round [61] log likelihood: -4590.819748
EM: Round [62] log likelihood: -4590.807405
EM: Round [63] log likelihood: -4590.795379
EM: Round [64] log likelihood: -4590.783653
EM: Round [65] log likelihood: -4590.772213
EM: Round [66] log likelihood: -4590.761044
EM: Round [67] log likelihood: -4590.750134
EM: Round [68] log likelihood: -4590.739469
EM: Round [69] log likelihood: -4590.729038
EM: Round [70] log likelihood: -4590.718830
EM: Round [71] log likelihood: -4590.708835
EM: Round [72] log likelihood: -4590.699043
EM: Round [73] log likelihood: -4590.689445
EM: Round [74] log likelihood: -4590.680032
EM: Round [75] log likelihood: -4590.670797
EM: Round [76] log likelihood: -4590.661732
EM: Round [77] log likelihood: -4590.652830
EM: Round [78] log likelihood: -4590.644084
EM: Round [79] log likelihood: -4590.635488
EM: Round [80] log likelihood: -4590.627035
EM: Round [81] log likelihood: -4590.618722
EM: Round [82] log likelihood: -4590.610541
EM: Round [83] log likelihood: -4590.602489
EM: Round [84] log likelihood: -4590.594561
EM: Round [85] log likelihood: -4590.586751
EM: Round [86] log likelihood: -4590.579057
EM: Round [87] log likelihood: -4590.571473
EM: Round [88] log likelihood: -4590.563997
EM: Round [89] log likelihood: -4590.556624
EM: Round [90] log likelihood: -4590.549352
EM: Round [91] log likelihood: -4590.542178
EM: Round [92] log likelihood: -4590.535097
EM: Round [93] log likelihood: -4590.528108
EM: Round [94] log likelihood: -4590.521208
EM: Round [95] log likelihood: -4590.514394
EM: Round [96] log likelihood: -4590.507663
EM: Round [97] log likelihood: -4590.501014
EM: Round [98] log likelihood: -4590.494444
EM: Round [99] log likelihood: -4590.487951
EM: Round [100] log likelihood: -4590.481534
EM: Round [101] log likelihood: -4590.475189
EM: Round [102] log likelihood: -4590.468916
EM: Round [103] log likelihood: -4590.462712
EM: Round [104] log likelihood: -4590.456576
EM: Round [105] log likelihood: -4590.450507
EM: Round [106] log likelihood: -4590.444502
EM: Round [107] log likelihood: -4590.438561
EM: Round [108] log likelihood: -4590.432682
EM: Round [109] log likelihood: -4590.426863
EM: Round [110] log likelihood: -4590.421104
EM: Round [111] log likelihood: -4590.415403
EM: Round [112] log likelihood: -4590.409759
EM: Round [113] log likelihood: -4590.404170
EM: Round [114] log likelihood: -4590.398637
EM: Round [115] log likelihood: -4590.393157
EM: Round [116] log likelihood: -4590.387729
EM: Round [117] log likelihood: -4590.382353
EM: Round [118] log likelihood: -4590.377028
EM: Round [119] log likelihood: -4590.371753
EM: Round [120] log likelihood: -4590.366526
EM: Round [121] log likelihood: -4590.361348
EM: Round [122] log likelihood: -4590.356216
EM: Round [123] log likelihood: -4590.351132
EM: Round [124] log likelihood: -4590.346092
EM: Round [125] log likelihood: -4590.341098
EM: Round [126] log likelihood: -4590.336148
EM: Round [127] log likelihood: -4590.331241
EM: Round [128] log likelihood: -4590.326377
EM: Round [129] log likelihood: -4590.321555
EM: Round [130] log likelihood: -4590.316775
EM: Round [131] log likelihood: -4590.312035
EM: Round [132] log likelihood: -4590.307336
EM: Round [133] log likelihood: -4590.302676
EM: Round [134] log likelihood: -4590.298056
EM: Round [135] log likelihood: -4590.293473
EM: Round [136] log likelihood: -4590.288929
EM: Round [137] log likelihood: -4590.284422
EM: Round [138] log likelihood: -4590.279952
EM: Round [139] log likelihood: -4590.275519
EM: Round [140] log likelihood: -4590.271121
EM: Round [141] log likelihood: -4590.266759
EM: Round [142] log likelihood: -4590.262431
EM: Round [143] log likelihood: -4590.258138
EM: Round [144] log likelihood: -4590.253879
EM: Round [145] log likelihood: -4590.249654
EM: Round [146] log likelihood: -4590.245462
EM: Round [147] log likelihood: -4590.241302
EM: Round [148] log likelihood: -4590.237175
EM: Round [149] log likelihood: -4590.233079
EM: Round [150] log likelihood: -4590.229016
EM: Round [151] log likelihood: -4590.224983
EM: Round [152] log likelihood: -4590.220981
EM: Round [153] log likelihood: -4590.217009
EM: Round [154] log likelihood: -4590.213067
EM: Round [155] log likelihood: -4590.209155
EM: Round [156] log likelihood: -4590.205272
EM: Round [157] log likelihood: -4590.201419
EM: Round [158] log likelihood: -4590.197593
EM: Round [159] log likelihood: -4590.193796
EM: Round [160] log likelihood: -4590.190027
EM: Round [161] log likelihood: -4590.186286
EM: Round [162] log likelihood: -4590.182571
EM: Round [163] log likelihood: -4590.178884
EM: Round [164] log likelihood: -4590.175224
EM: Round [165] log likelihood: -4590.171590
EM: Round [166] log likelihood: -4590.167982
EM: Round [167] log likelihood: -4590.164399
EM: Round [168] log likelihood: -4590.160843
EM: Round [169] log likelihood: -4590.157311
EM: Round [170] log likelihood: -4590.153805
EM: Round [171] log likelihood: -4590.150323
EM: Round [172] log likelihood: -4590.146866
EM: Round [173] log likelihood: -4590.143433
EM: Round [174] log likelihood: -4590.140024
EM: Round [175] log likelihood: -4590.136638
EM: Round [176] log likelihood: -4590.133276
EM: Round [177] log likelihood: -4590.129937
EM: Round [178] log likelihood: -4590.126622
EM: Round [179] log likelihood: -4590.123328
EM: Round [180] log likelihood: -4590.120058
EM: Round [181] log likelihood: -4590.116809
EM: Round [182] log likelihood: -4590.113583
EM: Round [183] log likelihood: -4590.110378
EM: Round [184] log likelihood: -4590.107195
EM: Round [185] log likelihood: -4590.104034
EM: Round [186] log likelihood: -4590.100893
EM: Round [187] log likelihood: -4590.097774
EM: Round [188] log likelihood: -4590.094675
EM: Round [189] log likelihood: -4590.091597
EM: Round [190] log likelihood: -4590.088539
EM: Round [191] log likelihood: -4590.085501
EM: Round [192] log likelihood: -4590.082483
EM: Round [193] log likelihood: -4590.079485
EM: Round [194] log likelihood: -4590.076507
EM: Round [195] log likelihood: -4590.073547
EM: Round [196] log likelihood: -4590.070608
EM: Round [197] log likelihood: -4590.067687
EM: Round [198] log likelihood: -4590.064785
EM: Round [199] log likelihood: -4590.061901
EM: Round [200] log likelihood: -4590.059036
EM: Round [201] log likelihood: -4590.056190
EM: Round [202] log likelihood: -4590.053361
EM: Round [203] log likelihood: -4590.050551
EM: Round [204] log likelihood: -4590.047758
EM: Round [205] log likelihood: -4590.044983
EM: Round [206] log likelihood: -4590.042226
EM: Round [207] log likelihood: -4590.039485
EM: Round [208] log likelihood: -4590.036762
EM: Round [209] log likelihood: -4590.034056
EM: Round [210] log likelihood: -4590.031367
EM: Round [211] log likelihood: -4590.028695
EM: Round [212] log likelihood: -4590.026039
EM: Round [213] log likelihood: -4590.023400
EM: Round [214] log likelihood: -4590.020777
EM: Round [215] log likelihood: -4590.018170
EM: Round [216] log likelihood: -4590.015579
EM: Round [217] log likelihood: -4590.013003
EM: Round [218] log likelihood: -4590.010444
EM: Round [219] log likelihood: -4590.007900
EM: Round [220] log likelihood: -4590.005372
EM: Round [221] log likelihood: -4590.002859
EM: Round [222] log likelihood: -4590.000361
EM: Round [223] log likelihood: -4589.997878
EM: Round [224] log likelihood: -4589.995410
EM: Round [225] log likelihood: -4589.992957
EM: Round [226] log likelihood: -4589.990518
EM: Round [227] log likelihood: -4589.988095
EM: Round [228] log likelihood: -4589.985685
EM: Round [229] log likelihood: -4589.983290
EM: Round [230] log likelihood: -4589.980909
EM: Round [231] log likelihood: -4589.978542
EM: Round [232] log likelihood: -4589.976189
EM: Round [233] log likelihood: -4589.973850
EM: Round [234] log likelihood: -4589.971525
EM: Round [235] log likelihood: -4589.969213
EM: Round [236] log likelihood: -4589.966915
EM: Round [237] log likelihood: -4589.964630
EM: Round [238] log likelihood: -4589.962358
EM: Round [239] log likelihood: -4589.960100
EM: Round [240] log likelihood: -4589.957855
EM: Round [241] log likelihood: -4589.955622
EM: Round [242] log likelihood: -4589.953403
EM: Round [243] log likelihood: -4589.951196
EM: Round [244] log likelihood: -4589.949002
EM: Round [245] log likelihood: -4589.946821
EM: Round [246] log likelihood: -4589.944652
EM: Round [247] log likelihood: -4589.942495
EM: Round [248] log likelihood: -4589.940351
EM: Round [249] log likelihood: -4589.938218
EM: Round [250] log likelihood: -4589.936098
EM: Round [251] log likelihood: -4589.933990
EM: Round [252] log likelihood: -4589.931894
EM: Round [253] log likelihood: -4589.929809
EM: Round [254] log likelihood: -4589.927737
EM: Round [255] log likelihood: -4589.925676
EM: Round [256] log likelihood: -4589.923626
EM: Round [257] log likelihood: -4589.921588
EM: Round [258] log likelihood: -4589.919561
EM: Round [259] log likelihood: -4589.917545
EM: Round [260] log likelihood: -4589.915541
EM: Round [261] log likelihood: -4589.913548
EM: Round [262] log likelihood: -4589.911566
EM: Round [263] log likelihood: -4589.909594
EM: Round [264] log likelihood: -4589.907634
EM: Round [265] log likelihood: -4589.905684
EM: Round [266] log likelihood: -4589.903745
EM: Round [267] log likelihood: -4589.901817
EM: Round [268] log likelihood: -4589.899899
EM: Round [269] log likelihood: -4589.897991
EM: Round [270] log likelihood: -4589.896094
EM: Round [271] log likelihood: -4589.894208
EM: Round [272] log likelihood: -4589.892331
EM: Round [273] log likelihood: -4589.890465
EM: Round [274] log likelihood: -4589.888608
EM: Round [275] log likelihood: -4589.886762
EM: Round [276] log likelihood: -4589.884926
EM: Round [277] log likelihood: -4589.883099
EM: Round [278] log likelihood: -4589.881283
EM: Round [279] log likelihood: -4589.879476
EM: Round [280] log likelihood: -4589.877678
EM: Round [281] log likelihood: -4589.875891
EM: Round [282] log likelihood: -4589.874112
EM: Round [283] log likelihood: -4589.872344
EM: Round [284] log likelihood: -4589.870584
EM: Round [285] log likelihood: -4589.868834
EM: Round [286] log likelihood: -4589.867093
EM: Round [287] log likelihood: -4589.865362
EM: Round [288] log likelihood: -4589.863639
EM: Round [289] log likelihood: -4589.861926
EM: Round [290] log likelihood: -4589.860221
EM: Round [291] log likelihood: -4589.858526
EM: Round [292] log likelihood: -4589.856839
EM: Round [293] log likelihood: -4589.855161
EM: Round [294] log likelihood: -4589.853492
EM: Round [295] log likelihood: -4589.851832
EM: Round [296] log likelihood: -4589.850180
EM: Round [297] log likelihood: -4589.848537
EM: Round [298] log likelihood: -4589.846902
EM: Round [299] log likelihood: -4589.845276
EM: Round [300] log likelihood: -4589.843658
EM: Round [301] log likelihood: -4589.842048
EM: Round [302] log likelihood: -4589.840447
EM: Round [303] log likelihood: -4589.838854
EM: Round [304] log likelihood: -4589.837269
EM: Round [305] log likelihood: -4589.835692
EM: Round [306] log likelihood: -4589.834124
EM: Round [307] log likelihood: -4589.832563
EM: Round [308] log likelihood: -4589.831010
EM: Round [309] log likelihood: -4589.829466
EM: Round [310] log likelihood: -4589.827929
EM: Round [311] log likelihood: -4589.826399
EM: Round [312] log likelihood: -4589.824878
EM: Round [313] log likelihood: -4589.823364
EM: Round [314] log likelihood: -4589.821858
EM: Round [315] log likelihood: -4589.820360
EM: Round [316] log likelihood: -4589.818869
EM: Round [317] log likelihood: -4589.817385
EM: Round [318] log likelihood: -4589.815909
EM: Round [319] log likelihood: -4589.814441
EM: Round [320] log likelihood: -4589.812979
EM: Round [321] log likelihood: -4589.811526
EM: Round [322] log likelihood: -4589.810079
EM: Round [323] log likelihood: -4589.808639
EM: Round [324] log likelihood: -4589.807207
EM: Round [325] log likelihood: -4589.805782
EM: Round [326] log likelihood: -4589.804364
EM: Round [327] log likelihood: -4589.802953
EM: Round [328] log likelihood: -4589.801549
EM: Round [329] log likelihood: -4589.800151
EM: Round [330] log likelihood: -4589.798761
EM: Round [331] log likelihood: -4589.797378
EM: Round [332] log likelihood: -4589.796001
EM: Round [333] log likelihood: -4589.794631
EM: Round [334] log likelihood: -4589.793268
EM: Round [335] log likelihood: -4589.791912
EM: Round [336] log likelihood: -4589.790562
EM: Round [337] log likelihood: -4589.789219
EM: Round [338] log likelihood: -4589.787882
EM: Round [339] log likelihood: -4589.786552
EM: Round [340] log likelihood: -4589.785228
EM: Round [341] log likelihood: -4589.783911
EM: Round [342] log likelihood: -4589.782600
EM: Round [343] log likelihood: -4589.781296
EM: Round [344] log likelihood: -4589.779998
EM: Round [345] log likelihood: -4589.778706
EM: Round [346] log likelihood: -4589.777420
EM: Round [347] log likelihood: -4589.776141
EM: Round [348] log likelihood: -4589.774867
EM: Round [349] log likelihood: -4589.773600
EM: Round [350] log likelihood: -4589.772339
EM: Round [351] log likelihood: -4589.771084
EM: Round [352] log likelihood: -4589.769835
EM: Round [353] log likelihood: -4589.768592
EM: Round [354] log likelihood: -4589.767355
EM: Round [355] log likelihood: -4589.766124
EM: Round [356] log likelihood: -4589.764899
EM: Round [357] log likelihood: -4589.763679
EM: Round [358] log likelihood: -4589.762466
EM: Round [359] log likelihood: -4589.761258
EM: Round [360] log likelihood: -4589.760056
EM: Round [361] log likelihood: -4589.758859
EM: Round [362] log likelihood: -4589.757668
EM: Round [363] log likelihood: -4589.756483
EM: Round [364] log likelihood: -4589.755304
EM: Round [365] log likelihood: -4589.754130
EM: Round [366] log likelihood: -4589.752961
EM: Round [367] log likelihood: -4589.751798
EM: Round [368] log likelihood: -4589.750641
EM: Round [369] log likelihood: -4589.749489
EM: Round [370] log likelihood: -4589.748342
EM: Round [371] log likelihood: -4589.747201
EM: Round [372] log likelihood: -4589.746065
EM: Round [373] log likelihood: -4589.744934
EM: Round [374] log likelihood: -4589.743809
EM: Round [375] log likelihood: -4589.742689
EM: Round [376] log likelihood: -4589.741574
EM: Round [377] log likelihood: -4589.740464
EM: Round [378] log likelihood: -4589.739360
EM: Round [379] log likelihood: -4589.738261
EM: Round [380] log likelihood: -4589.737166
EM: Round [381] log likelihood: -4589.736077
EM: Round [382] log likelihood: -4589.734993
EM: Round [383] log likelihood: -4589.733914
EM: Round [384] log likelihood: -4589.732840
EM: Round [385] log likelihood: -4589.731770
EM: Round [386] log likelihood: -4589.730706
EM: Round [387] log likelihood: -4589.729647
EM: Round [388] log likelihood: -4589.728592
EM: Round [389] log likelihood: -4589.727542
EM: Round [390] log likelihood: -4589.726498
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EM: Round [850] log likelihood: -4589.514477
EM: Round [851] log likelihood: -4589.514312
EM: Round [852] log likelihood: -4589.514149
EM: Round [853] log likelihood: -4589.513986
EM: Round [854] log likelihood: -4589.513823
EM: Round [855] log likelihood: -4589.513662
EM: Round [856] log likelihood: -4589.513500
EM: Round [857] log likelihood: -4589.513340
EM: Round [858] log likelihood: -4589.513180
EM: Round [859] log likelihood: -4589.513020
EM: Round [860] log likelihood: -4589.512862
EM: Round [861] log likelihood: -4589.512703
EM: Round [862] log likelihood: -4589.512546
EM: Round [863] log likelihood: -4589.512389
EM: Round [864] log likelihood: -4589.512232
EM: Round [865] log likelihood: -4589.512076
EM: Round [866] log likelihood: -4589.511921
EM: Round [867] log likelihood: -4589.511766
EM: Round [868] log likelihood: -4589.511612
EM: Round [869] log likelihood: -4589.511458
EM: Round [870] log likelihood: -4589.511305
EM: Round [871] log likelihood: -4589.511153
EM: Round [872] log likelihood: -4589.511001
EM: Round [873] log likelihood: -4589.510850
EM: Round [874] log likelihood: -4589.510699
EM: Round [875] log likelihood: -4589.510549
EM: Round [876] log likelihood: -4589.510399
EM: Round [877] log likelihood: -4589.510250
EM: Round [878] log likelihood: -4589.510101
EM: Round [879] log likelihood: -4589.509953
EM: Round [880] log likelihood: -4589.509806
EM: Round [881] log likelihood: -4589.509659
EM: Round [882] log likelihood: -4589.509512
EM: Round [883] log likelihood: -4589.509367
EM: Round [884] log likelihood: -4589.509221
EM: Round [885] log likelihood: -4589.509076
EM: Round [886] log likelihood: -4589.508932
EM: Round [887] log likelihood: -4589.508788
EM: Round [888] log likelihood: -4589.508645
EM: Round [889] log likelihood: -4589.508503
EM: Round [890] log likelihood: -4589.508361
EM: Round [891] log likelihood: -4589.508219
EM: Round [892] log likelihood: -4589.508078
EM: Round [893] log likelihood: -4589.507937
EM: Round [894] log likelihood: -4589.507797
EM: Round [895] log likelihood: -4589.507658
EM: Round [896] log likelihood: -4589.507519
EM: Round [897] log likelihood: -4589.507380
EM: Round [898] log likelihood: -4589.507242
EM: Round [899] log likelihood: -4589.507105
EM: Round [900] log likelihood: -4589.506968
EM: Round [901] log likelihood: -4589.506831
EM: Round [902] log likelihood: -4589.506695
EM: Round [903] log likelihood: -4589.506560
EM: Round [904] log likelihood: -4589.506425
EM: Round [905] log likelihood: -4589.506290
EM: Round [906] log likelihood: -4589.506156
EM: Round [907] log likelihood: -4589.506023
EM: Round [908] log likelihood: -4589.505890
EM: Round [909] log likelihood: -4589.505758
EM: Round [910] log likelihood: -4589.505625
EM: Round [911] log likelihood: -4589.505494
EM: Round [912] log likelihood: -4589.505363
EM: Round [913] log likelihood: -4589.505232
EM: Round [914] log likelihood: -4589.505102
EM: Round [915] log likelihood: -4589.504973
EM: Round [916] log likelihood: -4589.504844
EM: Round [917] log likelihood: -4589.504715
EM: Round [918] log likelihood: -4589.504587
EM: Round [919] log likelihood: -4589.504459
EM: Round [920] log likelihood: -4589.504332
EM: Round [921] log likelihood: -4589.504205
EM: Round [922] log likelihood: -4589.504079
EM: Round [923] log likelihood: -4589.503953
EM: Round [924] log likelihood: -4589.503827
EM: Round [925] log likelihood: -4589.503703
EM: Round [926] log likelihood: -4589.503578
EM: Round [927] log likelihood: -4589.503454
EM: Round [928] log likelihood: -4589.503330
EM: Round [929] log likelihood: -4589.503207
EM: Round [930] log likelihood: -4589.503085
EM: Round [931] log likelihood: -4589.502963
EM: Round [932] log likelihood: -4589.502841
EM: Round [933] log likelihood: -4589.502720
EM: Round [934] log likelihood: -4589.502599
EM: Round [935] log likelihood: -4589.502478
EM: Round [936] log likelihood: -4589.502358
EM: Round [937] log likelihood: -4589.502239
EM: Round [938] log likelihood: -4589.502120
EM: Round [939] log likelihood: -4589.502001
EM: Round [940] log likelihood: -4589.501883
EM: Round [941] log likelihood: -4589.501765
EM: Round [942] log likelihood: -4589.501648
EM: Round [943] log likelihood: -4589.501531
EM: Round [944] log likelihood: -4589.501414
EM: Round [945] log likelihood: -4589.501298
EM: Round [946] log likelihood: -4589.501182
EM: Round [947] log likelihood: -4589.501067
EM: Round [948] log likelihood: -4589.500952
EM: Round [949] log likelihood: -4589.500838
EM: Round [950] log likelihood: -4589.500724
EM: Round [951] log likelihood: -4589.500611
EM: Round [952] log likelihood: -4589.500497
EM: Round [953] log likelihood: -4589.500385
EM: Round [954] log likelihood: -4589.500272
EM: Round [955] log likelihood: -4589.500160
EM: Round [956] log likelihood: -4589.500049
EM: Round [957] log likelihood: -4589.499938
EM: Round [958] log likelihood: -4589.499827
EM: Round [959] log likelihood: -4589.499717
EM: Round [960] log likelihood: -4589.499607
EM: Round [961] log likelihood: -4589.499498
EM: Round [962] log likelihood: -4589.499389
EM: Round [963] log likelihood: -4589.499280
EM: Round [964] log likelihood: -4589.499172
EM: Round [965] log likelihood: -4589.499064
EM: Round [966] log likelihood: -4589.498956
EM: Round [967] log likelihood: -4589.498849
EM: Round [968] log likelihood: -4589.498742
EM: Round [969] log likelihood: -4589.498636
EM: Round [970] log likelihood: -4589.498530
EM: Round [971] log likelihood: -4589.498425
EM: Round [972] log likelihood: -4589.498320
EM: Round [973] log likelihood: -4589.498215
EM: Round [974] log likelihood: -4589.498110
EM: Round [975] log likelihood: -4589.498006
EM: Round [976] log likelihood: -4589.497903
EM: Round [977] log likelihood: -4589.497800
EM: Round [978] log likelihood: -4589.497697
EM: Round [979] log likelihood: -4589.497594
EM: Round [980] log likelihood: -4589.497492
EM: Round [981] log likelihood: -4589.497390
EM: Round [982] log likelihood: -4589.497289
EM: Round [983] log likelihood: -4589.497188
EM: Round [984] log likelihood: -4589.497087
EM: Round [985] log likelihood: -4589.496987
EM: Round [986] log likelihood: -4589.496887
EM: Stopping iterations at round 986 due to insufficient improvement in likelihood.
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.8hThpsG6it/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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.8hThpsG6it/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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/tih_rna_sample_00570_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.8hThpsG6it/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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.8hThpsG6it/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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.8hThpsG6it/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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa > /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/tih_rna_sample_00570_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir
-done, see /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2895.159577
EM: Round [1] log likelihood: -2895.086857
EM: Round [2] log likelihood: -2895.086251
EM: Round [3] log likelihood: -2895.086243
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1_1.fastp.fastq.gz: 295858521
Execution Time = 5.52 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa --gtf /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf  > /tmp/nxf.8hThpsG6it/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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fa --gtf /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.gtf  > /tmp/nxf.8hThpsG6it/fi_workdir/microH.dat
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.8hThpsG6it/fi_workdir/microH.dat /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/fi_workdir/microH.dat /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.8hThpsG6it --json_outfile /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00570_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.8hThpsG6it --json_outfile /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00570_B23MVV7LT4_1
Running: touch /tmp/nxf.8hThpsG6it/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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00570_B23MVV7LT4_1 --html_output /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_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.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00570_B23MVV7LT4_1 --html_output /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
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 [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.8hThpsG6it/ctat_genome_lib_build_dir > /tmp/nxf.8hThpsG6it/tih_rna_sample_00570_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.8hThpsG6it/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory