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/d0/a680a30a94746fd8d45fbd5217d779/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/a680a30a94746fd8d45fbd5217d779/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/2671da15fea1972ecb405f532e2990/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/2671da15fea1972ecb405f532e2990/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/1ad22dd3c7a5aef133bb8daca66ee9/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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 aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf > /tmp/nxf.XcfmkvrFWR/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf > /tmp/nxf.XcfmkvrFWR/cytoBand.txt
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed
-parsing GTF file: /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.XcfmkvrFWR/fi_workdir --reads "/tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 03 21:42:40 ..... started STAR run
Jun 03 21:42:40 ..... loading genome
Jun 03 21:44:23 ... generating Suffix Array index
Jun 03 21:48:08 ... completed Suffix Array index
Jun 03 21:48:08 ..... processing annotations GTF
Jun 03 21:48:08 ..... inserting junctions into the genome indices
Jun 03 21:49:10 ..... started mapping
Jun 03 22:56:05 ..... finished mapping
Jun 03 22:56:06 ..... started sorting BAM
Jun 03 22:56:07 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
Execution Time = 73.47 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.XcfmkvrFWR/fi_workdir --reads "/tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
22:56:13 : INFO : Done.
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[950000]   -done parsing /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'per_id < 96' => 3438,
          'num genes matched < 2' => 20,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 20,
          'small anchor length' => 28,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
          ' ** passed ** ' => 2710,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 246,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 20,
          'exons hit < 2' => 1,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
          'low complexity anchor region' => 4,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 150,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 54,
          'excessive soft clipping' => 5466,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8
        };
-writing fusion junction support info.
Execution Time = 0.51 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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-fusion SPANNING read extraction for scaff: GUCY1B2--NKAIN2

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[206000]   -fusion SPANNING read extraction for scaff: NECTIN3--PHLDB2

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[21000]   -fusion SPANNING read extraction for scaff: NECTIN3--PLCXD2

[1000]   
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[205000]   
[206000]   -fusion SPANNING read extraction for scaff: PHLDB2--NECTIN3

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[21000]   -fusion SPANNING read extraction for scaff: PLCXD2--NECTIN3

[1000]   
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[29000]   -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146

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[33000]   
[34000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

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[60000]   
[61000]   
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[63000]   
[64000]   
[65000]   -fusion SPANNING read extraction for scaff: SELENOO--TUBGCP6

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[53000]   
[54000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[94000]   -fusion SPANNING read extraction for scaff: SVEP1--MYLK

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[37000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[32000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[18000]   -fusion SPANNING read extraction for scaff: UBE2Q2P1--GOLGA6L10
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 6887
        };
Execution Time = 1.49 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4456.448106
EM: Round [1] log likelihood: -4448.303876
EM: Round [2] log likelihood: -4447.060826
EM: Round [3] log likelihood: -4446.799529
EM: Round [4] log likelihood: -4446.696716
EM: Round [5] log likelihood: -4446.640472
EM: Round [6] log likelihood: -4446.606416
EM: Round [7] log likelihood: -4446.584338
EM: Round [8] log likelihood: -4446.568896
EM: Round [9] log likelihood: -4446.557175
EM: Round [10] log likelihood: -4446.547563
EM: Round [11] log likelihood: -4446.539169
EM: Round [12] log likelihood: -4446.531497
EM: Round [13] log likelihood: -4446.524272
EM: Round [14] log likelihood: -4446.517339
EM: Round [15] log likelihood: -4446.510611
EM: Round [16] log likelihood: -4446.504041
EM: Round [17] log likelihood: -4446.497598
EM: Round [18] log likelihood: -4446.491268
EM: Round [19] log likelihood: -4446.485040
EM: Round [20] log likelihood: -4446.478908
EM: Round [21] log likelihood: -4446.472867
EM: Round [22] log likelihood: -4446.466915
EM: Round [23] log likelihood: -4446.461048
EM: Round [24] log likelihood: -4446.455264
EM: Round [25] log likelihood: -4446.449563
EM: Round [26] log likelihood: -4446.443941
EM: Round [27] log likelihood: -4446.438398
EM: Round [28] log likelihood: -4446.432931
EM: Round [29] log likelihood: -4446.427540
EM: Round [30] log likelihood: -4446.422223
EM: Round [31] log likelihood: -4446.416978
EM: Round [32] log likelihood: -4446.411804
EM: Round [33] log likelihood: -4446.406700
EM: Round [34] log likelihood: -4446.401665
EM: Round [35] log likelihood: -4446.396697
EM: Round [36] log likelihood: -4446.391794
EM: Round [37] log likelihood: -4446.386957
EM: Round [38] log likelihood: -4446.382183
EM: Round [39] log likelihood: -4446.377472
EM: Round [40] log likelihood: -4446.372822
EM: Round [41] log likelihood: -4446.368233
EM: Round [42] log likelihood: -4446.363702
EM: Round [43] log likelihood: -4446.359230
EM: Round [44] log likelihood: -4446.354816
EM: Round [45] log likelihood: -4446.350457
EM: Round [46] log likelihood: -4446.346154
EM: Round [47] log likelihood: -4446.341905
EM: Round [48] log likelihood: -4446.337710
EM: Round [49] log likelihood: -4446.333567
EM: Round [50] log likelihood: -4446.329476
EM: Round [51] log likelihood: -4446.325435
EM: Round [52] log likelihood: -4446.321445
EM: Round [53] log likelihood: -4446.317504
EM: Round [54] log likelihood: -4446.313611
EM: Round [55] log likelihood: -4446.309766
EM: Round [56] log likelihood: -4446.305968
EM: Round [57] log likelihood: -4446.302216
EM: Round [58] log likelihood: -4446.298509
EM: Round [59] log likelihood: -4446.294847
EM: Round [60] log likelihood: -4446.291229
EM: Round [61] log likelihood: -4446.287654
EM: Round [62] log likelihood: -4446.284122
EM: Round [63] log likelihood: -4446.280632
EM: Round [64] log likelihood: -4446.277183
EM: Round [65] log likelihood: -4446.273775
EM: Round [66] log likelihood: -4446.270406
EM: Round [67] log likelihood: -4446.267078
EM: Round [68] log likelihood: -4446.263788
EM: Round [69] log likelihood: -4446.260536
EM: Round [70] log likelihood: -4446.257323
EM: Round [71] log likelihood: -4446.254146
EM: Round [72] log likelihood: -4446.251006
EM: Round [73] log likelihood: -4446.247902
EM: Round [74] log likelihood: -4446.244834
EM: Round [75] log likelihood: -4446.241800
EM: Round [76] log likelihood: -4446.238802
EM: Round [77] log likelihood: -4446.235837
EM: Round [78] log likelihood: -4446.232906
EM: Round [79] log likelihood: -4446.230008
EM: Round [80] log likelihood: -4446.227142
EM: Round [81] log likelihood: -4446.224309
EM: Round [82] log likelihood: -4446.221508
EM: Round [83] log likelihood: -4446.218737
EM: Round [84] log likelihood: -4446.215998
EM: Round [85] log likelihood: -4446.213289
EM: Round [86] log likelihood: -4446.210610
EM: Round [87] log likelihood: -4446.207960
EM: Round [88] log likelihood: -4446.205340
EM: Round [89] log likelihood: -4446.202749
EM: Round [90] log likelihood: -4446.200186
EM: Round [91] log likelihood: -4446.197651
EM: Round [92] log likelihood: -4446.195143
EM: Round [93] log likelihood: -4446.192663
EM: Round [94] log likelihood: -4446.190210
EM: Round [95] log likelihood: -4446.187783
EM: Round [96] log likelihood: -4446.185382
EM: Round [97] log likelihood: -4446.183008
EM: Round [98] log likelihood: -4446.180659
EM: Round [99] log likelihood: -4446.178334
EM: Round [100] log likelihood: -4446.176035
EM: Round [101] log likelihood: -4446.173761
EM: Round [102] log likelihood: -4446.171510
EM: Round [103] log likelihood: -4446.169284
EM: Round [104] log likelihood: -4446.167081
EM: Round [105] log likelihood: -4446.164901
EM: Round [106] log likelihood: -4446.162745
EM: Round [107] log likelihood: -4446.160611
EM: Round [108] log likelihood: -4446.158499
EM: Round [109] log likelihood: -4446.156410
EM: Round [110] log likelihood: -4446.154342
EM: Round [111] log likelihood: -4446.152296
EM: Round [112] log likelihood: -4446.150272
EM: Round [113] log likelihood: -4446.148268
EM: Round [114] log likelihood: -4446.146285
EM: Round [115] log likelihood: -4446.144323
EM: Round [116] log likelihood: -4446.142381
EM: Round [117] log likelihood: -4446.140459
EM: Round [118] log likelihood: -4446.138557
EM: Round [119] log likelihood: -4446.136675
EM: Round [120] log likelihood: -4446.134811
EM: Round [121] log likelihood: -4446.132967
EM: Round [122] log likelihood: -4446.131142
EM: Round [123] log likelihood: -4446.129335
EM: Round [124] log likelihood: -4446.127547
EM: Round [125] log likelihood: -4446.125777
EM: Round [126] log likelihood: -4446.124025
EM: Round [127] log likelihood: -4446.122290
EM: Round [128] log likelihood: -4446.120573
EM: Round [129] log likelihood: -4446.118874
EM: Round [130] log likelihood: -4446.117191
EM: Round [131] log likelihood: -4446.115526
EM: Round [132] log likelihood: -4446.113877
EM: Round [133] log likelihood: -4446.112245
EM: Round [134] log likelihood: -4446.110629
EM: Round [135] log likelihood: -4446.109029
EM: Round [136] log likelihood: -4446.107446
EM: Round [137] log likelihood: -4446.105878
EM: Round [138] log likelihood: -4446.104325
EM: Round [139] log likelihood: -4446.102788
EM: Round [140] log likelihood: -4446.101267
EM: Round [141] log likelihood: -4446.099760
EM: Round [142] log likelihood: -4446.098268
EM: Round [143] log likelihood: -4446.096791
EM: Round [144] log likelihood: -4446.095329
EM: Round [145] log likelihood: -4446.093881
EM: Round [146] log likelihood: -4446.092447
EM: Round [147] log likelihood: -4446.091027
EM: Round [148] log likelihood: -4446.089621
EM: Round [149] log likelihood: -4446.088229
EM: Round [150] log likelihood: -4446.086851
EM: Round [151] log likelihood: -4446.085486
EM: Round [152] log likelihood: -4446.084134
EM: Round [153] log likelihood: -4446.082796
EM: Round [154] log likelihood: -4446.081470
EM: Round [155] log likelihood: -4446.080158
EM: Round [156] log likelihood: -4446.078858
EM: Round [157] log likelihood: -4446.077570
EM: Round [158] log likelihood: -4446.076296
EM: Round [159] log likelihood: -4446.075033
EM: Round [160] log likelihood: -4446.073783
EM: Round [161] log likelihood: -4446.072544
EM: Round [162] log likelihood: -4446.071318
EM: Round [163] log likelihood: -4446.070103
EM: Round [164] log likelihood: -4446.068900
EM: Round [165] log likelihood: -4446.067709
EM: Round [166] log likelihood: -4446.066529
EM: Round [167] log likelihood: -4446.065360
EM: Round [168] log likelihood: -4446.064203
EM: Round [169] log likelihood: -4446.063056
EM: Round [170] log likelihood: -4446.061921
EM: Round [171] log likelihood: -4446.060796
EM: Round [172] log likelihood: -4446.059682
EM: Round [173] log likelihood: -4446.058579
EM: Round [174] log likelihood: -4446.057486
EM: Round [175] log likelihood: -4446.056403
EM: Round [176] log likelihood: -4446.055331
EM: Round [177] log likelihood: -4446.054268
EM: Round [178] log likelihood: -4446.053216
EM: Round [179] log likelihood: -4446.052174
EM: Round [180] log likelihood: -4446.051141
EM: Round [181] log likelihood: -4446.050119
EM: Round [182] log likelihood: -4446.049106
EM: Round [183] log likelihood: -4446.048102
EM: Round [184] log likelihood: -4446.047108
EM: Round [185] log likelihood: -4446.046123
EM: Round [186] log likelihood: -4446.045148
EM: Round [187] log likelihood: -4446.044181
EM: Round [188] log likelihood: -4446.043224
EM: Round [189] log likelihood: -4446.042275
EM: Round [190] log likelihood: -4446.041336
EM: Round [191] log likelihood: -4446.040405
EM: Round [192] log likelihood: -4446.039483
EM: Round [193] log likelihood: -4446.038569
EM: Round [194] log likelihood: -4446.037664
EM: Round [195] log likelihood: -4446.036768
EM: Round [196] log likelihood: -4446.035879
EM: Round [197] log likelihood: -4446.034999
EM: Round [198] log likelihood: -4446.034128
EM: Round [199] log likelihood: -4446.033264
EM: Round [200] log likelihood: -4446.032408
EM: Round [201] log likelihood: -4446.031560
EM: Round [202] log likelihood: -4446.030720
EM: Round [203] log likelihood: -4446.029888
EM: Round [204] log likelihood: -4446.029063
EM: Round [205] log likelihood: -4446.028246
EM: Round [206] log likelihood: -4446.027436
EM: Round [207] log likelihood: -4446.026634
EM: Round [208] log likelihood: -4446.025840
EM: Round [209] log likelihood: -4446.025052
EM: Round [210] log likelihood: -4446.024272
EM: Round [211] log likelihood: -4446.023499
EM: Round [212] log likelihood: -4446.022733
EM: Round [213] log likelihood: -4446.021974
EM: Round [214] log likelihood: -4446.021222
EM: Round [215] log likelihood: -4446.020477
EM: Round [216] log likelihood: -4446.019739
EM: Round [217] log likelihood: -4446.019007
EM: Round [218] log likelihood: -4446.018283
EM: Round [219] log likelihood: -4446.017564
EM: Round [220] log likelihood: -4446.016853
EM: Round [221] log likelihood: -4446.016147
EM: Round [222] log likelihood: -4446.015449
EM: Round [223] log likelihood: -4446.014756
EM: Round [224] log likelihood: -4446.014070
EM: Round [225] log likelihood: -4446.013390
EM: Round [226] log likelihood: -4446.012716
EM: Round [227] log likelihood: -4446.012049
EM: Round [228] log likelihood: -4446.011387
EM: Round [229] log likelihood: -4446.010731
EM: Round [230] log likelihood: -4446.010082
EM: Round [231] log likelihood: -4446.009438
EM: Round [232] log likelihood: -4446.008800
EM: Round [233] log likelihood: -4446.008168
EM: Round [234] log likelihood: -4446.007541
EM: Round [235] log likelihood: -4446.006920
EM: Round [236] log likelihood: -4446.006305
EM: Round [237] log likelihood: -4446.005695
EM: Round [238] log likelihood: -4446.005091
EM: Round [239] log likelihood: -4446.004492
EM: Round [240] log likelihood: -4446.003899
EM: Round [241] log likelihood: -4446.003311
EM: Round [242] log likelihood: -4446.002728
EM: Round [243] log likelihood: -4446.002151
EM: Round [244] log likelihood: -4446.001578
EM: Round [245] log likelihood: -4446.001011
EM: Round [246] log likelihood: -4446.000449
EM: Round [247] log likelihood: -4445.999892
EM: Round [248] log likelihood: -4445.999340
EM: Round [249] log likelihood: -4445.998793
EM: Round [250] log likelihood: -4445.998250
EM: Round [251] log likelihood: -4445.997713
EM: Round [252] log likelihood: -4445.997180
EM: Round [253] log likelihood: -4445.996652
EM: Round [254] log likelihood: -4445.996129
EM: Round [255] log likelihood: -4445.995611
EM: Round [256] log likelihood: -4445.995097
EM: Round [257] log likelihood: -4445.994587
EM: Round [258] log likelihood: -4445.994083
EM: Round [259] log likelihood: -4445.993582
EM: Round [260] log likelihood: -4445.993086
EM: Round [261] log likelihood: -4445.992595
EM: Round [262] log likelihood: -4445.992108
EM: Round [263] log likelihood: -4445.991625
EM: Round [264] log likelihood: -4445.991147
EM: Round [265] log likelihood: -4445.990673
EM: Round [266] log likelihood: -4445.990203
EM: Round [267] log likelihood: -4445.989737
EM: Round [268] log likelihood: -4445.989275
EM: Round [269] log likelihood: -4445.988818
EM: Round [270] log likelihood: -4445.988364
EM: Round [271] log likelihood: -4445.987915
EM: Round [272] log likelihood: -4445.987469
EM: Round [273] log likelihood: -4445.987027
EM: Round [274] log likelihood: -4445.986590
EM: Round [275] log likelihood: -4445.986156
EM: Round [276] log likelihood: -4445.985726
EM: Round [277] log likelihood: -4445.985300
EM: Round [278] log likelihood: -4445.984877
EM: Round [279] log likelihood: -4445.984458
EM: Round [280] log likelihood: -4445.984043
EM: Round [281] log likelihood: -4445.983632
EM: Round [282] log likelihood: -4445.983224
EM: Round [283] log likelihood: -4445.982820
EM: Round [284] log likelihood: -4445.982419
EM: Round [285] log likelihood: -4445.982022
EM: Round [286] log likelihood: -4445.981629
EM: Round [287] log likelihood: -4445.981239
EM: Round [288] log likelihood: -4445.980852
EM: Round [289] log likelihood: -4445.980469
EM: Round [290] log likelihood: -4445.980089
EM: Round [291] log likelihood: -4445.979712
EM: Round [292] log likelihood: -4445.979339
EM: Round [293] log likelihood: -4445.978969
EM: Round [294] log likelihood: -4445.978602
EM: Round [295] log likelihood: -4445.978238
EM: Round [296] log likelihood: -4445.977878
EM: Round [297] log likelihood: -4445.977521
EM: Round [298] log likelihood: -4445.977167
EM: Round [299] log likelihood: -4445.976816
EM: Round [300] log likelihood: -4445.976468
EM: Round [301] log likelihood: -4445.976123
EM: Round [302] log likelihood: -4445.975781
EM: Round [303] log likelihood: -4445.975442
EM: Round [304] log likelihood: -4445.975106
EM: Round [305] log likelihood: -4445.974773
EM: Round [306] log likelihood: -4445.974443
EM: Round [307] log likelihood: -4445.974116
EM: Round [308] log likelihood: -4445.973792
EM: Round [309] log likelihood: -4445.973470
EM: Round [310] log likelihood: -4445.973151
EM: Round [311] log likelihood: -4445.972836
EM: Round [312] log likelihood: -4445.972522
EM: Round [313] log likelihood: -4445.972212
EM: Round [314] log likelihood: -4445.971904
EM: Round [315] log likelihood: -4445.971599
EM: Round [316] log likelihood: -4445.971297
EM: Round [317] log likelihood: -4445.970997
EM: Round [318] log likelihood: -4445.970700
EM: Round [319] log likelihood: -4445.970405
EM: Round [320] log likelihood: -4445.970113
EM: Round [321] log likelihood: -4445.969824
EM: Round [322] log likelihood: -4445.969537
EM: Round [323] log likelihood: -4445.969252
EM: Round [324] log likelihood: -4445.968970
EM: Round [325] log likelihood: -4445.968691
EM: Round [326] log likelihood: -4445.968414
EM: Round [327] log likelihood: -4445.968139
EM: Round [328] log likelihood: -4445.967867
EM: Round [329] log likelihood: -4445.967597
EM: Round [330] log likelihood: -4445.967329
EM: Round [331] log likelihood: -4445.967064
EM: Round [332] log likelihood: -4445.966801
EM: Round [333] log likelihood: -4445.966540
EM: Round [334] log likelihood: -4445.966281
EM: Round [335] log likelihood: -4445.966025
EM: Round [336] log likelihood: -4445.965771
EM: Round [337] log likelihood: -4445.965519
EM: Round [338] log likelihood: -4445.965270
EM: Round [339] log likelihood: -4445.965022
EM: Round [340] log likelihood: -4445.964777
EM: Round [341] log likelihood: -4445.964534
EM: Round [342] log likelihood: -4445.964292
EM: Round [343] log likelihood: -4445.964053
EM: Round [344] log likelihood: -4445.963816
EM: Round [345] log likelihood: -4445.963581
EM: Round [346] log likelihood: -4445.963349
EM: Round [347] log likelihood: -4445.963118
EM: Round [348] log likelihood: -4445.962889
EM: Round [349] log likelihood: -4445.962662
EM: Round [350] log likelihood: -4445.962437
EM: Round [351] log likelihood: -4445.962214
EM: Round [352] log likelihood: -4445.961993
EM: Round [353] log likelihood: -4445.961774
EM: Round [354] log likelihood: -4445.961556
EM: Round [355] log likelihood: -4445.961341
EM: Round [356] log likelihood: -4445.961127
EM: Round [357] log likelihood: -4445.960916
EM: Round [358] log likelihood: -4445.960706
EM: Round [359] log likelihood: -4445.960497
EM: Round [360] log likelihood: -4445.960291
EM: Round [361] log likelihood: -4445.960087
EM: Round [362] log likelihood: -4445.959884
EM: Round [363] log likelihood: -4445.959683
EM: Round [364] log likelihood: -4445.959484
EM: Round [365] log likelihood: -4445.959286
EM: Round [366] log likelihood: -4445.959090
EM: Round [367] log likelihood: -4445.958896
EM: Round [368] log likelihood: -4445.958703
EM: Round [369] log likelihood: -4445.958512
EM: Round [370] log likelihood: -4445.958323
EM: Round [371] log likelihood: -4445.958136
EM: Round [372] log likelihood: -4445.957950
EM: Round [373] log likelihood: -4445.957765
EM: Round [374] log likelihood: -4445.957582
EM: Round [375] log likelihood: -4445.957401
EM: Round [376] log likelihood: -4445.957221
EM: Round [377] log likelihood: -4445.957043
EM: Round [378] log likelihood: -4445.956867
EM: Round [379] log likelihood: -4445.956691
EM: Round [380] log likelihood: -4445.956518
EM: Round [381] log likelihood: -4445.956346
EM: Round [382] log likelihood: -4445.956175
EM: Round [383] log likelihood: -4445.956006
EM: Round [384] log likelihood: -4445.955838
EM: Round [385] log likelihood: -4445.955672
EM: Round [386] log likelihood: -4445.955507
EM: Round [387] log likelihood: -4445.955343
EM: Round [388] log likelihood: -4445.955181
EM: Round [389] log likelihood: -4445.955021
EM: Round [390] log likelihood: -4445.954861
EM: Round [391] log likelihood: -4445.954704
EM: Round [392] log likelihood: -4445.954547
EM: Round [393] log likelihood: -4445.954392
EM: Round [394] log likelihood: -4445.954238
EM: Round [395] log likelihood: -4445.954085
EM: Round [396] log likelihood: -4445.953934
EM: Round [397] log likelihood: -4445.953784
EM: Round [398] log likelihood: -4445.953635
EM: Round [399] log likelihood: -4445.953488
EM: Round [400] log likelihood: -4445.953342
EM: Round [401] log likelihood: -4445.953197
EM: Round [402] log likelihood: -4445.953053
EM: Round [403] log likelihood: -4445.952910
EM: Round [404] log likelihood: -4445.952769
EM: Round [405] log likelihood: -4445.952629
EM: Round [406] log likelihood: -4445.952490
EM: Round [407] log likelihood: -4445.952353
EM: Round [408] log likelihood: -4445.952216
EM: Round [409] log likelihood: -4445.952081
EM: Round [410] log likelihood: -4445.951947
EM: Round [411] log likelihood: -4445.951814
EM: Round [412] log likelihood: -4445.951682
EM: Round [413] log likelihood: -4445.951551
EM: Round [414] log likelihood: -4445.951421
EM: Round [415] log likelihood: -4445.951293
EM: Round [416] log likelihood: -4445.951165
EM: Round [417] log likelihood: -4445.951039
EM: Round [418] log likelihood: -4445.950914
EM: Round [419] log likelihood: -4445.950790
EM: Round [420] log likelihood: -4445.950666
EM: Round [421] log likelihood: -4445.950544
EM: Round [422] log likelihood: -4445.950423
EM: Round [423] log likelihood: -4445.950303
EM: Round [424] log likelihood: -4445.950184
EM: Round [425] log likelihood: -4445.950066
EM: Round [426] log likelihood: -4445.949949
EM: Round [427] log likelihood: -4445.949833
EM: Round [428] log likelihood: -4445.949718
EM: Round [429] log likelihood: -4445.949604
EM: Round [430] log likelihood: -4445.949491
EM: Round [431] log likelihood: -4445.949379
EM: Round [432] log likelihood: -4445.949268
EM: Round [433] log likelihood: -4445.949158
EM: Round [434] log likelihood: -4445.949049
EM: Round [435] log likelihood: -4445.948940
EM: Round [436] log likelihood: -4445.948833
EM: Round [437] log likelihood: -4445.948726
EM: Round [438] log likelihood: -4445.948621
EM: Round [439] log likelihood: -4445.948516
EM: Round [440] log likelihood: -4445.948412
EM: Round [441] log likelihood: -4445.948309
EM: Round [442] log likelihood: -4445.948207
EM: Round [443] log likelihood: -4445.948106
EM: Round [444] log likelihood: -4445.948006
EM: Round [445] log likelihood: -4445.947906
EM: Stopping iterations at round 445 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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa > /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir
-done, see /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -4273.162346
EM: Round [1] log likelihood: -4266.248751
EM: Round [2] log likelihood: -4265.318131
EM: Round [3] log likelihood: -4265.220162
EM: Round [4] log likelihood: -4265.205285
EM: Round [5] log likelihood: -4265.197072
EM: Round [6] log likelihood: -4265.189453
EM: Round [7] log likelihood: -4265.181987
EM: Round [8] log likelihood: -4265.174640
EM: Round [9] log likelihood: -4265.167408
EM: Round [10] log likelihood: -4265.160289
EM: Round [11] log likelihood: -4265.153278
EM: Round [12] log likelihood: -4265.146375
EM: Round [13] log likelihood: -4265.139577
EM: Round [14] log likelihood: -4265.132881
EM: Round [15] log likelihood: -4265.126286
EM: Round [16] log likelihood: -4265.119788
EM: Round [17] log likelihood: -4265.113387
EM: Round [18] log likelihood: -4265.107079
EM: Round [19] log likelihood: -4265.100864
EM: Round [20] log likelihood: -4265.094738
EM: Round [21] log likelihood: -4265.088701
EM: Round [22] log likelihood: -4265.082751
EM: Round [23] log likelihood: -4265.076885
EM: Round [24] log likelihood: -4265.071103
EM: Round [25] log likelihood: -4265.065401
EM: Round [26] log likelihood: -4265.059780
EM: Round [27] log likelihood: -4265.054237
EM: Round [28] log likelihood: -4265.048770
EM: Round [29] log likelihood: -4265.043379
EM: Round [30] log likelihood: -4265.038062
EM: Round [31] log likelihood: -4265.032817
EM: Round [32] log likelihood: -4265.027643
EM: Round [33] log likelihood: -4265.022539
EM: Round [34] log likelihood: -4265.017504
EM: Round [35] log likelihood: -4265.012536
EM: Round [36] log likelihood: -4265.007634
EM: Round [37] log likelihood: -4265.002796
EM: Round [38] log likelihood: -4264.998022
EM: Round [39] log likelihood: -4264.993311
EM: Round [40] log likelihood: -4264.988661
EM: Round [41] log likelihood: -4264.984072
EM: Round [42] log likelihood: -4264.979541
EM: Round [43] log likelihood: -4264.975069
EM: Round [44] log likelihood: -4264.970655
EM: Round [45] log likelihood: -4264.966296
EM: Round [46] log likelihood: -4264.961993
EM: Round [47] log likelihood: -4264.957744
EM: Round [48] log likelihood: -4264.953549
EM: Round [49] log likelihood: -4264.949406
EM: Round [50] log likelihood: -4264.945315
EM: Round [51] log likelihood: -4264.941275
EM: Round [52] log likelihood: -4264.937284
EM: Round [53] log likelihood: -4264.933343
EM: Round [54] log likelihood: -4264.929450
EM: Round [55] log likelihood: -4264.925605
EM: Round [56] log likelihood: -4264.921807
EM: Round [57] log likelihood: -4264.918055
EM: Round [58] log likelihood: -4264.914348
EM: Round [59] log likelihood: -4264.910686
EM: Round [60] log likelihood: -4264.907068
EM: Round [61] log likelihood: -4264.903493
EM: Round [62] log likelihood: -4264.899961
EM: Round [63] log likelihood: -4264.896471
EM: Round [64] log likelihood: -4264.893022
EM: Round [65] log likelihood: -4264.889614
EM: Round [66] log likelihood: -4264.886245
EM: Round [67] log likelihood: -4264.882917
EM: Round [68] log likelihood: -4264.879627
EM: Round [69] log likelihood: -4264.876375
EM: Round [70] log likelihood: -4264.873162
EM: Round [71] log likelihood: -4264.869985
EM: Round [72] log likelihood: -4264.866845
EM: Round [73] log likelihood: -4264.863741
EM: Round [74] log likelihood: -4264.860673
EM: Round [75] log likelihood: -4264.857639
EM: Round [76] log likelihood: -4264.854641
EM: Round [77] log likelihood: -4264.851676
EM: Round [78] log likelihood: -4264.848745
EM: Round [79] log likelihood: -4264.845847
EM: Round [80] log likelihood: -4264.842982
EM: Round [81] log likelihood: -4264.840148
EM: Round [82] log likelihood: -4264.837347
EM: Round [83] log likelihood: -4264.834576
EM: Round [84] log likelihood: -4264.831837
EM: Round [85] log likelihood: -4264.829128
EM: Round [86] log likelihood: -4264.826449
EM: Round [87] log likelihood: -4264.823800
EM: Round [88] log likelihood: -4264.821179
EM: Round [89] log likelihood: -4264.818588
EM: Round [90] log likelihood: -4264.816025
EM: Round [91] log likelihood: -4264.813490
EM: Round [92] log likelihood: -4264.810982
EM: Round [93] log likelihood: -4264.808502
EM: Round [94] log likelihood: -4264.806049
EM: Round [95] log likelihood: -4264.803622
EM: Round [96] log likelihood: -4264.801221
EM: Round [97] log likelihood: -4264.798847
EM: Round [98] log likelihood: -4264.796498
EM: Round [99] log likelihood: -4264.794174
EM: Round [100] log likelihood: -4264.791874
EM: Round [101] log likelihood: -4264.789600
EM: Round [102] log likelihood: -4264.787349
EM: Round [103] log likelihood: -4264.785123
EM: Round [104] log likelihood: -4264.782920
EM: Round [105] log likelihood: -4264.780740
EM: Round [106] log likelihood: -4264.778584
EM: Round [107] log likelihood: -4264.776450
EM: Round [108] log likelihood: -4264.774338
EM: Round [109] log likelihood: -4264.772249
EM: Round [110] log likelihood: -4264.770181
EM: Round [111] log likelihood: -4264.768135
EM: Round [112] log likelihood: -4264.766111
EM: Round [113] log likelihood: -4264.764107
EM: Round [114] log likelihood: -4264.762125
EM: Round [115] log likelihood: -4264.760162
EM: Round [116] log likelihood: -4264.758220
EM: Round [117] log likelihood: -4264.756298
EM: Round [118] log likelihood: -4264.754396
EM: Round [119] log likelihood: -4264.752514
EM: Round [120] log likelihood: -4264.750651
EM: Round [121] log likelihood: -4264.748806
EM: Round [122] log likelihood: -4264.746981
EM: Round [123] log likelihood: -4264.745174
EM: Round [124] log likelihood: -4264.743386
EM: Round [125] log likelihood: -4264.741616
EM: Round [126] log likelihood: -4264.739864
EM: Round [127] log likelihood: -4264.738129
EM: Round [128] log likelihood: -4264.736413
EM: Round [129] log likelihood: -4264.734713
EM: Round [130] log likelihood: -4264.733031
EM: Round [131] log likelihood: -4264.731365
EM: Round [132] log likelihood: -4264.729716
EM: Round [133] log likelihood: -4264.728084
EM: Round [134] log likelihood: -4264.726468
EM: Round [135] log likelihood: -4264.724869
EM: Round [136] log likelihood: -4264.723285
EM: Round [137] log likelihood: -4264.721717
EM: Round [138] log likelihood: -4264.720164
EM: Round [139] log likelihood: -4264.718628
EM: Round [140] log likelihood: -4264.717106
EM: Round [141] log likelihood: -4264.715599
EM: Round [142] log likelihood: -4264.714107
EM: Round [143] log likelihood: -4264.712630
EM: Round [144] log likelihood: -4264.711168
EM: Round [145] log likelihood: -4264.709720
EM: Round [146] log likelihood: -4264.708286
EM: Round [147] log likelihood: -4264.706866
EM: Round [148] log likelihood: -4264.705461
EM: Round [149] log likelihood: -4264.704069
EM: Round [150] log likelihood: -4264.702690
EM: Round [151] log likelihood: -4264.701325
EM: Round [152] log likelihood: -4264.699973
EM: Round [153] log likelihood: -4264.698635
EM: Round [154] log likelihood: -4264.697309
EM: Round [155] log likelihood: -4264.695997
EM: Round [156] log likelihood: -4264.694697
EM: Round [157] log likelihood: -4264.693410
EM: Round [158] log likelihood: -4264.692135
EM: Round [159] log likelihood: -4264.690872
EM: Round [160] log likelihood: -4264.689622
EM: Round [161] log likelihood: -4264.688384
EM: Round [162] log likelihood: -4264.687157
EM: Round [163] log likelihood: -4264.685943
EM: Round [164] log likelihood: -4264.684740
EM: Round [165] log likelihood: -4264.683548
EM: Round [166] log likelihood: -4264.682368
EM: Round [167] log likelihood: -4264.681199
EM: Round [168] log likelihood: -4264.680042
EM: Round [169] log likelihood: -4264.678895
EM: Round [170] log likelihood: -4264.677760
EM: Round [171] log likelihood: -4264.676635
EM: Round [172] log likelihood: -4264.675521
EM: Round [173] log likelihood: -4264.674418
EM: Round [174] log likelihood: -4264.673325
EM: Round [175] log likelihood: -4264.672242
EM: Round [176] log likelihood: -4264.671170
EM: Round [177] log likelihood: -4264.670107
EM: Round [178] log likelihood: -4264.669055
EM: Round [179] log likelihood: -4264.668013
EM: Round [180] log likelihood: -4264.666981
EM: Round [181] log likelihood: -4264.665958
EM: Round [182] log likelihood: -4264.664945
EM: Round [183] log likelihood: -4264.663941
EM: Round [184] log likelihood: -4264.662947
EM: Round [185] log likelihood: -4264.661962
EM: Round [186] log likelihood: -4264.660987
EM: Round [187] log likelihood: -4264.660020
EM: Round [188] log likelihood: -4264.659063
EM: Round [189] log likelihood: -4264.658115
EM: Round [190] log likelihood: -4264.657175
EM: Round [191] log likelihood: -4264.656244
EM: Round [192] log likelihood: -4264.655322
EM: Round [193] log likelihood: -4264.654409
EM: Round [194] log likelihood: -4264.653504
EM: Round [195] log likelihood: -4264.652607
EM: Round [196] log likelihood: -4264.651719
EM: Round [197] log likelihood: -4264.650839
EM: Round [198] log likelihood: -4264.649967
EM: Round [199] log likelihood: -4264.649103
EM: Round [200] log likelihood: -4264.648247
EM: Round [201] log likelihood: -4264.647399
EM: Round [202] log likelihood: -4264.646559
EM: Round [203] log likelihood: -4264.645727
EM: Round [204] log likelihood: -4264.644902
EM: Round [205] log likelihood: -4264.644085
EM: Round [206] log likelihood: -4264.643276
EM: Round [207] log likelihood: -4264.642473
EM: Round [208] log likelihood: -4264.641679
EM: Round [209] log likelihood: -4264.640891
EM: Round [210] log likelihood: -4264.640111
EM: Round [211] log likelihood: -4264.639338
EM: Round [212] log likelihood: -4264.638572
EM: Round [213] log likelihood: -4264.637813
EM: Round [214] log likelihood: -4264.637061
EM: Round [215] log likelihood: -4264.636316
EM: Round [216] log likelihood: -4264.635578
EM: Round [217] log likelihood: -4264.634847
EM: Round [218] log likelihood: -4264.634122
EM: Round [219] log likelihood: -4264.633403
EM: Round [220] log likelihood: -4264.632692
EM: Round [221] log likelihood: -4264.631987
EM: Round [222] log likelihood: -4264.631288
EM: Round [223] log likelihood: -4264.630595
EM: Round [224] log likelihood: -4264.629909
EM: Round [225] log likelihood: -4264.629229
EM: Round [226] log likelihood: -4264.628555
EM: Round [227] log likelihood: -4264.627888
EM: Round [228] log likelihood: -4264.627226
EM: Round [229] log likelihood: -4264.626571
EM: Round [230] log likelihood: -4264.625921
EM: Round [231] log likelihood: -4264.625277
EM: Round [232] log likelihood: -4264.624639
EM: Round [233] log likelihood: -4264.624007
EM: Round [234] log likelihood: -4264.623380
EM: Round [235] log likelihood: -4264.622760
EM: Round [236] log likelihood: -4264.622144
EM: Round [237] log likelihood: -4264.621535
EM: Round [238] log likelihood: -4264.620930
EM: Round [239] log likelihood: -4264.620332
EM: Round [240] log likelihood: -4264.619738
EM: Round [241] log likelihood: -4264.619150
EM: Round [242] log likelihood: -4264.618567
EM: Round [243] log likelihood: -4264.617990
EM: Round [244] log likelihood: -4264.617417
EM: Round [245] log likelihood: -4264.616850
EM: Round [246] log likelihood: -4264.616288
EM: Round [247] log likelihood: -4264.615731
EM: Round [248] log likelihood: -4264.615179
EM: Round [249] log likelihood: -4264.614632
EM: Round [250] log likelihood: -4264.614089
EM: Round [251] log likelihood: -4264.613552
EM: Round [252] log likelihood: -4264.613019
EM: Round [253] log likelihood: -4264.612491
EM: Round [254] log likelihood: -4264.611968
EM: Round [255] log likelihood: -4264.611450
EM: Round [256] log likelihood: -4264.610936
EM: Round [257] log likelihood: -4264.610426
EM: Round [258] log likelihood: -4264.609922
EM: Round [259] log likelihood: -4264.609421
EM: Round [260] log likelihood: -4264.608926
EM: Round [261] log likelihood: -4264.608434
EM: Round [262] log likelihood: -4264.607947
EM: Round [263] log likelihood: -4264.607464
EM: Round [264] log likelihood: -4264.606986
EM: Round [265] log likelihood: -4264.606512
EM: Round [266] log likelihood: -4264.606042
EM: Round [267] log likelihood: -4264.605576
EM: Round [268] log likelihood: -4264.605114
EM: Round [269] log likelihood: -4264.604657
EM: Round [270] log likelihood: -4264.604203
EM: Round [271] log likelihood: -4264.603754
EM: Round [272] log likelihood: -4264.603308
EM: Round [273] log likelihood: -4264.602866
EM: Round [274] log likelihood: -4264.602429
EM: Round [275] log likelihood: -4264.601995
EM: Round [276] log likelihood: -4264.601565
EM: Round [277] log likelihood: -4264.601139
EM: Round [278] log likelihood: -4264.600716
EM: Round [279] log likelihood: -4264.600297
EM: Round [280] log likelihood: -4264.599882
EM: Round [281] log likelihood: -4264.599471
EM: Round [282] log likelihood: -4264.599063
EM: Round [283] log likelihood: -4264.598659
EM: Round [284] log likelihood: -4264.598259
EM: Round [285] log likelihood: -4264.597861
EM: Round [286] log likelihood: -4264.597468
EM: Round [287] log likelihood: -4264.597078
EM: Round [288] log likelihood: -4264.596691
EM: Round [289] log likelihood: -4264.596308
EM: Round [290] log likelihood: -4264.595928
EM: Round [291] log likelihood: -4264.595551
EM: Round [292] log likelihood: -4264.595178
EM: Round [293] log likelihood: -4264.594808
EM: Round [294] log likelihood: -4264.594441
EM: Round [295] log likelihood: -4264.594078
EM: Round [296] log likelihood: -4264.593717
EM: Round [297] log likelihood: -4264.593360
EM: Round [298] log likelihood: -4264.593006
EM: Round [299] log likelihood: -4264.592655
EM: Round [300] log likelihood: -4264.592307
EM: Round [301] log likelihood: -4264.591962
EM: Round [302] log likelihood: -4264.591620
EM: Round [303] log likelihood: -4264.591281
EM: Round [304] log likelihood: -4264.590945
EM: Round [305] log likelihood: -4264.590612
EM: Round [306] log likelihood: -4264.590282
EM: Round [307] log likelihood: -4264.589955
EM: Round [308] log likelihood: -4264.589631
EM: Round [309] log likelihood: -4264.589309
EM: Round [310] log likelihood: -4264.588991
EM: Round [311] log likelihood: -4264.588675
EM: Round [312] log likelihood: -4264.588362
EM: Round [313] log likelihood: -4264.588051
EM: Round [314] log likelihood: -4264.587743
EM: Round [315] log likelihood: -4264.587438
EM: Round [316] log likelihood: -4264.587136
EM: Round [317] log likelihood: -4264.586836
EM: Round [318] log likelihood: -4264.586539
EM: Round [319] log likelihood: -4264.586244
EM: Round [320] log likelihood: -4264.585952
EM: Round [321] log likelihood: -4264.585663
EM: Round [322] log likelihood: -4264.585376
EM: Round [323] log likelihood: -4264.585091
EM: Round [324] log likelihood: -4264.584809
EM: Round [325] log likelihood: -4264.584530
EM: Round [326] log likelihood: -4264.584253
EM: Round [327] log likelihood: -4264.583978
EM: Round [328] log likelihood: -4264.583706
EM: Round [329] log likelihood: -4264.583436
EM: Round [330] log likelihood: -4264.583168
EM: Round [331] log likelihood: -4264.582903
EM: Round [332] log likelihood: -4264.582640
EM: Round [333] log likelihood: -4264.582379
EM: Round [334] log likelihood: -4264.582120
EM: Round [335] log likelihood: -4264.581864
EM: Round [336] log likelihood: -4264.581610
EM: Round [337] log likelihood: -4264.581358
EM: Round [338] log likelihood: -4264.581109
EM: Round [339] log likelihood: -4264.580861
EM: Round [340] log likelihood: -4264.580616
EM: Round [341] log likelihood: -4264.580373
EM: Round [342] log likelihood: -4264.580132
EM: Round [343] log likelihood: -4264.579892
EM: Round [344] log likelihood: -4264.579656
EM: Round [345] log likelihood: -4264.579421
EM: Round [346] log likelihood: -4264.579188
EM: Round [347] log likelihood: -4264.578957
EM: Round [348] log likelihood: -4264.578728
EM: Round [349] log likelihood: -4264.578501
EM: Round [350] log likelihood: -4264.578276
EM: Round [351] log likelihood: -4264.578053
EM: Round [352] log likelihood: -4264.577832
EM: Round [353] log likelihood: -4264.577613
EM: Round [354] log likelihood: -4264.577395
EM: Round [355] log likelihood: -4264.577180
EM: Round [356] log likelihood: -4264.576966
EM: Round [357] log likelihood: -4264.576755
EM: Round [358] log likelihood: -4264.576545
EM: Round [359] log likelihood: -4264.576337
EM: Round [360] log likelihood: -4264.576130
EM: Round [361] log likelihood: -4264.575926
EM: Round [362] log likelihood: -4264.575723
EM: Round [363] log likelihood: -4264.575522
EM: Round [364] log likelihood: -4264.575323
EM: Round [365] log likelihood: -4264.575125
EM: Round [366] log likelihood: -4264.574929
EM: Round [367] log likelihood: -4264.574735
EM: Round [368] log likelihood: -4264.574542
EM: Round [369] log likelihood: -4264.574352
EM: Round [370] log likelihood: -4264.574162
EM: Round [371] log likelihood: -4264.573975
EM: Round [372] log likelihood: -4264.573789
EM: Round [373] log likelihood: -4264.573604
EM: Round [374] log likelihood: -4264.573421
EM: Round [375] log likelihood: -4264.573240
EM: Round [376] log likelihood: -4264.573060
EM: Round [377] log likelihood: -4264.572882
EM: Round [378] log likelihood: -4264.572706
EM: Round [379] log likelihood: -4264.572531
EM: Round [380] log likelihood: -4264.572357
EM: Round [381] log likelihood: -4264.572185
EM: Round [382] log likelihood: -4264.572014
EM: Round [383] log likelihood: -4264.571845
EM: Round [384] log likelihood: -4264.571677
EM: Round [385] log likelihood: -4264.571511
EM: Round [386] log likelihood: -4264.571346
EM: Round [387] log likelihood: -4264.571183
EM: Round [388] log likelihood: -4264.571021
EM: Round [389] log likelihood: -4264.570860
EM: Round [390] log likelihood: -4264.570701
EM: Round [391] log likelihood: -4264.570543
EM: Round [392] log likelihood: -4264.570386
EM: Round [393] log likelihood: -4264.570231
EM: Round [394] log likelihood: -4264.570077
EM: Round [395] log likelihood: -4264.569924
EM: Round [396] log likelihood: -4264.569773
EM: Round [397] log likelihood: -4264.569623
EM: Round [398] log likelihood: -4264.569474
EM: Round [399] log likelihood: -4264.569327
EM: Round [400] log likelihood: -4264.569181
EM: Round [401] log likelihood: -4264.569036
EM: Round [402] log likelihood: -4264.568892
EM: Round [403] log likelihood: -4264.568750
EM: Round [404] log likelihood: -4264.568608
EM: Round [405] log likelihood: -4264.568468
EM: Round [406] log likelihood: -4264.568329
EM: Round [407] log likelihood: -4264.568192
EM: Round [408] log likelihood: -4264.568055
EM: Round [409] log likelihood: -4264.567920
EM: Round [410] log likelihood: -4264.567786
EM: Round [411] log likelihood: -4264.567653
EM: Round [412] log likelihood: -4264.567521
EM: Round [413] log likelihood: -4264.567390
EM: Round [414] log likelihood: -4264.567260
EM: Round [415] log likelihood: -4264.567132
EM: Round [416] log likelihood: -4264.567004
EM: Round [417] log likelihood: -4264.566878
EM: Round [418] log likelihood: -4264.566753
EM: Round [419] log likelihood: -4264.566629
EM: Round [420] log likelihood: -4264.566506
EM: Round [421] log likelihood: -4264.566383
EM: Round [422] log likelihood: -4264.566262
EM: Round [423] log likelihood: -4264.566142
EM: Round [424] log likelihood: -4264.566023
EM: Round [425] log likelihood: -4264.565905
EM: Round [426] log likelihood: -4264.565788
EM: Round [427] log likelihood: -4264.565672
EM: Round [428] log likelihood: -4264.565557
EM: Round [429] log likelihood: -4264.565443
EM: Round [430] log likelihood: -4264.565330
EM: Round [431] log likelihood: -4264.565218
EM: Round [432] log likelihood: -4264.565107
EM: Round [433] log likelihood: -4264.564997
EM: Round [434] log likelihood: -4264.564888
EM: Round [435] log likelihood: -4264.564779
EM: Round [436] log likelihood: -4264.564672
EM: Round [437] log likelihood: -4264.564565
EM: Round [438] log likelihood: -4264.564460
EM: Round [439] log likelihood: -4264.564355
EM: Round [440] log likelihood: -4264.564251
EM: Round [441] log likelihood: -4264.564148
EM: Round [442] log likelihood: -4264.564046
EM: Round [443] log likelihood: -4264.563945
EM: Round [444] log likelihood: -4264.563845
EM: Round [445] log likelihood: -4264.563746
EM: Stopping iterations at round 445 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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296338986
Execution Time = 6.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf  > /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.gtf  > /tmp/nxf.XcfmkvrFWR/fi_workdir/microH.dat
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.XcfmkvrFWR/fi_workdir/microH.dat /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/fi_workdir/microH.dat /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.XcfmkvrFWR --json_outfile /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.XcfmkvrFWR --json_outfile /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1
Running: touch /tmp/nxf.XcfmkvrFWR/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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1 --html_output /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1 --html_output /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000189136.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000226240.2]
WARNING, no entry stored in dbm for [ENSG00000254560.6]
WARNING, no entry stored in dbm for [ENSG00000237978.6]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000229140.11]
WARNING, no entry stored in dbm for [ENSG00000229140.11]
WARNING, no entry stored in dbm for [ENSG00000229140.11]
WARNING, no entry stored in dbm for [ENSG00000229140.11]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000249909.1]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
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]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.XcfmkvrFWR/ctat_genome_lib_build_dir > /tmp/nxf.XcfmkvrFWR/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.XcfmkvrFWR/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory