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/1e/a9548ea73fd20188d092f30fe5c111/tih_rna_sample_00467_B23WHTKLT4_2.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0273f44f0780547e572af1c83ea576/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/0751ba1aa97ae6194fed2d06e9b492/tih_rna_sample_00467_B23WHTKLT4_2_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0273f44f0780547e572af1c83ea576/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/0751ba1aa97ae6194fed2d06e9b492/tih_rna_sample_00467_B23WHTKLT4_2_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00467_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00467_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.gtf
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf > /tmp/nxf.1wx8ERHk48/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf > /tmp/nxf.1wx8ERHk48/cytoBand.txt
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.bed
-parsing GTF file: /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.bed
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.bed > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.bed > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00467_B23WHTKLT4_2.star --out_dir /tmp/nxf.1wx8ERHk48/fi_workdir --reads "/tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:11:38 ..... started STAR run
Jun 08 10:11:38 ..... loading genome
Jun 08 10:13:18 ... generating Suffix Array index
Jun 08 10:17:02 ... completed Suffix Array index
Jun 08 10:17:03 ..... processing annotations GTF
Jun 08 10:17:03 ..... inserting junctions into the genome indices
Jun 08 10:18:03 ..... started mapping
Jun 08 11:10:52 ..... finished mapping
Jun 08 11:10:53 ..... started sorting BAM
Jun 08 11:10:54 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00467_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00467_B23WHTKLT4_2.star.sortedByCoord.out.bam
Execution Time = 59.29 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00467_B23WHTKLT4_2.star --out_dir /tmp/nxf.1wx8ERHk48/fi_workdir --reads "/tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
11:11:00 : INFO : Done.
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

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[1150000]   -done parsing /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'small anchor length' => 24,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
          ' ** passed ** ' => 5630,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 19,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 87,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 72,
          'excessive soft clipping' => 15975,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 48,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 20,
          'low complexity anchor region' => 50,
          'seq-similar region overlap' => 291,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 384,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 123,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 158,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
          'per_id < 96' => 10399
        };
-writing fusion junction support info.
Execution Time = 0.59 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[141000]   -fusion SPANNING read extraction for scaff: DIP2B--RPRD2

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[58000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[56000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[1000]   
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[49000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[49000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[47000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[41000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[650000]   -fusion SPANNING read extraction for scaff: RPL14--ATN1

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

[1000]   
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[19000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 48085,
          'lacks exon overlap' => 7137
        };
Execution Time = 1.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2679.116046
EM: Round [1] log likelihood: -2679.024769
EM: Round [2] log likelihood: -2678.936017
EM: Round [3] log likelihood: -2678.849698
EM: Round [4] log likelihood: -2678.765726
EM: Round [5] log likelihood: -2678.684019
EM: Round [6] log likelihood: -2678.604496
EM: Round [7] log likelihood: -2678.527084
EM: Round [8] log likelihood: -2678.451710
EM: Round [9] log likelihood: -2678.378306
EM: Round [10] log likelihood: -2678.306808
EM: Round [11] log likelihood: -2678.237152
EM: Round [12] log likelihood: -2678.169278
EM: Round [13] log likelihood: -2678.103130
EM: Round [14] log likelihood: -2678.038652
EM: Round [15] log likelihood: -2677.975792
EM: Round [16] log likelihood: -2677.914500
EM: Round [17] log likelihood: -2677.854728
EM: Round [18] log likelihood: -2677.796428
EM: Round [19] log likelihood: -2677.739557
EM: Round [20] log likelihood: -2677.684071
EM: Round [21] log likelihood: -2677.629930
EM: Round [22] log likelihood: -2677.577094
EM: Round [23] log likelihood: -2677.525524
EM: Round [24] log likelihood: -2677.475185
EM: Round [25] log likelihood: -2677.426041
EM: Round [26] log likelihood: -2677.378057
EM: Round [27] log likelihood: -2677.331202
EM: Round [28] log likelihood: -2677.285443
EM: Round [29] log likelihood: -2677.240750
EM: Round [30] log likelihood: -2677.197093
EM: Round [31] log likelihood: -2677.154445
EM: Round [32] log likelihood: -2677.112777
EM: Round [33] log likelihood: -2677.072064
EM: Round [34] log likelihood: -2677.032279
EM: Round [35] log likelihood: -2676.993398
EM: Round [36] log likelihood: -2676.955397
EM: Round [37] log likelihood: -2676.918253
EM: Round [38] log likelihood: -2676.881943
EM: Round [39] log likelihood: -2676.846446
EM: Round [40] log likelihood: -2676.811741
EM: Round [41] log likelihood: -2676.777808
EM: Round [42] log likelihood: -2676.744626
EM: Round [43] log likelihood: -2676.712177
EM: Round [44] log likelihood: -2676.680442
EM: Round [45] log likelihood: -2676.649403
EM: Round [46] log likelihood: -2676.619044
EM: Round [47] log likelihood: -2676.589346
EM: Round [48] log likelihood: -2676.560294
EM: Round [49] log likelihood: -2676.531873
EM: Round [50] log likelihood: -2676.504066
EM: Round [51] log likelihood: -2676.476858
EM: Round [52] log likelihood: -2676.450236
EM: Round [53] log likelihood: -2676.424184
EM: Round [54] log likelihood: -2676.398690
EM: Round [55] log likelihood: -2676.373740
EM: Round [56] log likelihood: -2676.349321
EM: Round [57] log likelihood: -2676.325420
EM: Round [58] log likelihood: -2676.302026
EM: Round [59] log likelihood: -2676.279127
EM: Round [60] log likelihood: -2676.256710
EM: Round [61] log likelihood: -2676.234765
EM: Round [62] log likelihood: -2676.213281
EM: Round [63] log likelihood: -2676.192247
EM: Round [64] log likelihood: -2676.171652
EM: Round [65] log likelihood: -2676.151488
EM: Round [66] log likelihood: -2676.131743
EM: Round [67] log likelihood: -2676.112408
EM: Round [68] log likelihood: -2676.093475
EM: Round [69] log likelihood: -2676.074934
EM: Round [70] log likelihood: -2676.056776
EM: Round [71] log likelihood: -2676.038992
EM: Round [72] log likelihood: -2676.021575
EM: Round [73] log likelihood: -2676.004516
EM: Round [74] log likelihood: -2675.987806
EM: Round [75] log likelihood: -2675.971440
EM: Round [76] log likelihood: -2675.955408
EM: Round [77] log likelihood: -2675.939703
EM: Round [78] log likelihood: -2675.924319
EM: Round [79] log likelihood: -2675.909248
EM: Round [80] log likelihood: -2675.894483
EM: Round [81] log likelihood: -2675.880018
EM: Round [82] log likelihood: -2675.865846
EM: Round [83] log likelihood: -2675.851961
EM: Round [84] log likelihood: -2675.838357
EM: Round [85] log likelihood: -2675.825028
EM: Round [86] log likelihood: -2675.811967
EM: Round [87] log likelihood: -2675.799169
EM: Round [88] log likelihood: -2675.786629
EM: Round [89] log likelihood: -2675.774340
EM: Round [90] log likelihood: -2675.762298
EM: Round [91] log likelihood: -2675.750498
EM: Round [92] log likelihood: -2675.738933
EM: Round [93] log likelihood: -2675.727600
EM: Round [94] log likelihood: -2675.716493
EM: Round [95] log likelihood: -2675.705607
EM: Round [96] log likelihood: -2675.694939
EM: Round [97] log likelihood: -2675.684482
EM: Round [98] log likelihood: -2675.674234
EM: Round [99] log likelihood: -2675.664189
EM: Round [100] log likelihood: -2675.654344
EM: Round [101] log likelihood: -2675.644693
EM: Round [102] log likelihood: -2675.635234
EM: Round [103] log likelihood: -2675.625962
EM: Round [104] log likelihood: -2675.616873
EM: Round [105] log likelihood: -2675.607964
EM: Round [106] log likelihood: -2675.599231
EM: Round [107] log likelihood: -2675.590669
EM: Round [108] log likelihood: -2675.582277
EM: Round [109] log likelihood: -2675.574049
EM: Round [110] log likelihood: -2675.565984
EM: Round [111] log likelihood: -2675.558077
EM: Round [112] log likelihood: -2675.550325
EM: Round [113] log likelihood: -2675.542725
EM: Round [114] log likelihood: -2675.535274
EM: Round [115] log likelihood: -2675.527970
EM: Round [116] log likelihood: -2675.520808
EM: Round [117] log likelihood: -2675.513786
EM: Round [118] log likelihood: -2675.506902
EM: Round [119] log likelihood: -2675.500152
EM: Round [120] log likelihood: -2675.493534
EM: Round [121] log likelihood: -2675.487045
EM: Round [122] log likelihood: -2675.480682
EM: Round [123] log likelihood: -2675.474444
EM: Round [124] log likelihood: -2675.468327
EM: Round [125] log likelihood: -2675.462329
EM: Round [126] log likelihood: -2675.456448
EM: Round [127] log likelihood: -2675.450681
EM: Round [128] log likelihood: -2675.445026
EM: Round [129] log likelihood: -2675.439481
EM: Round [130] log likelihood: -2675.434043
EM: Round [131] log likelihood: -2675.428711
EM: Round [132] log likelihood: -2675.423483
EM: Round [133] log likelihood: -2675.418355
EM: Round [134] log likelihood: -2675.413327
EM: Round [135] log likelihood: -2675.408397
EM: Round [136] log likelihood: -2675.403561
EM: Round [137] log likelihood: -2675.398819
EM: Round [138] log likelihood: -2675.394169
EM: Round [139] log likelihood: -2675.389609
EM: Round [140] log likelihood: -2675.385137
EM: Round [141] log likelihood: -2675.380751
EM: Round [142] log likelihood: -2675.376449
EM: Round [143] log likelihood: -2675.372231
EM: Round [144] log likelihood: -2675.368094
EM: Round [145] log likelihood: -2675.364037
EM: Round [146] log likelihood: -2675.360057
EM: Round [147] log likelihood: -2675.356155
EM: Round [148] log likelihood: -2675.352327
EM: Round [149] log likelihood: -2675.348574
EM: Round [150] log likelihood: -2675.344892
EM: Round [151] log likelihood: -2675.341281
EM: Round [152] log likelihood: -2675.337740
EM: Round [153] log likelihood: -2675.334266
EM: Round [154] log likelihood: -2675.330860
EM: Round [155] log likelihood: -2675.327518
EM: Round [156] log likelihood: -2675.324241
EM: Round [157] log likelihood: -2675.321027
EM: Round [158] log likelihood: -2675.317874
EM: Round [159] log likelihood: -2675.314782
EM: Round [160] log likelihood: -2675.311749
EM: Round [161] log likelihood: -2675.308774
EM: Round [162] log likelihood: -2675.305857
EM: Round [163] log likelihood: -2675.302995
EM: Round [164] log likelihood: -2675.300187
EM: Round [165] log likelihood: -2675.297434
EM: Round [166] log likelihood: -2675.294733
EM: Round [167] log likelihood: -2675.292084
EM: Round [168] log likelihood: -2675.289486
EM: Round [169] log likelihood: -2675.286937
EM: Round [170] log likelihood: -2675.284437
EM: Round [171] log likelihood: -2675.281985
EM: Round [172] log likelihood: -2675.279580
EM: Round [173] log likelihood: -2675.277220
EM: Round [174] log likelihood: -2675.274906
EM: Round [175] log likelihood: -2675.272636
EM: Round [176] log likelihood: -2675.270409
EM: Round [177] log likelihood: -2675.268225
EM: Round [178] log likelihood: -2675.266082
EM: Round [179] log likelihood: -2675.263980
EM: Round [180] log likelihood: -2675.261919
EM: Round [181] log likelihood: -2675.259896
EM: Round [182] log likelihood: -2675.257912
EM: Round [183] log likelihood: -2675.255966
EM: Round [184] log likelihood: -2675.254057
EM: Round [185] log likelihood: -2675.252185
EM: Round [186] log likelihood: -2675.250348
EM: Round [187] log likelihood: -2675.248546
EM: Round [188] log likelihood: -2675.246778
EM: Round [189] log likelihood: -2675.245045
EM: Round [190] log likelihood: -2675.243344
EM: Round [191] log likelihood: -2675.241675
EM: Round [192] log likelihood: -2675.240038
EM: Round [193] log likelihood: -2675.238433
EM: Round [194] log likelihood: -2675.236858
EM: Round [195] log likelihood: -2675.235312
EM: Round [196] log likelihood: -2675.233797
EM: Round [197] log likelihood: -2675.232310
EM: Round [198] log likelihood: -2675.230851
EM: Round [199] log likelihood: -2675.229420
EM: Round [200] log likelihood: -2675.228016
EM: Round [201] log likelihood: -2675.226639
EM: Round [202] log likelihood: -2675.225288
EM: Round [203] log likelihood: -2675.223963
EM: Round [204] log likelihood: -2675.222663
EM: Round [205] log likelihood: -2675.221388
EM: Round [206] log likelihood: -2675.220137
EM: Round [207] log likelihood: -2675.218909
EM: Round [208] log likelihood: -2675.217705
EM: Round [209] log likelihood: -2675.216524
EM: Round [210] log likelihood: -2675.215365
EM: Round [211] log likelihood: -2675.214228
EM: Round [212] log likelihood: -2675.213113
EM: Round [213] log likelihood: -2675.212019
EM: Round [214] log likelihood: -2675.210946
EM: Round [215] log likelihood: -2675.209893
EM: Round [216] log likelihood: -2675.208860
EM: Round [217] log likelihood: -2675.207846
EM: Round [218] log likelihood: -2675.206852
EM: Round [219] log likelihood: -2675.205877
EM: Round [220] log likelihood: -2675.204920
EM: Round [221] log likelihood: -2675.203982
EM: Round [222] log likelihood: -2675.203061
EM: Round [223] log likelihood: -2675.202157
EM: Round [224] log likelihood: -2675.201271
EM: Round [225] log likelihood: -2675.200401
EM: Round [226] log likelihood: -2675.199548
EM: Round [227] log likelihood: -2675.198712
EM: Round [228] log likelihood: -2675.197891
EM: Round [229] log likelihood: -2675.197085
EM: Round [230] log likelihood: -2675.196295
EM: Round [231] log likelihood: -2675.195520
EM: Round [232] log likelihood: -2675.194759
EM: Round [233] log likelihood: -2675.194013
EM: Round [234] log likelihood: -2675.193281
EM: Round [235] log likelihood: -2675.192563
EM: Round [236] log likelihood: -2675.191859
EM: Round [237] log likelihood: -2675.191167
EM: Round [238] log likelihood: -2675.190489
EM: Round [239] log likelihood: -2675.189824
EM: Round [240] log likelihood: -2675.189171
EM: Round [241] log likelihood: -2675.188531
EM: Round [242] log likelihood: -2675.187903
EM: Round [243] log likelihood: -2675.187287
EM: Round [244] log likelihood: -2675.186682
EM: Round [245] log likelihood: -2675.186089
EM: Round [246] log likelihood: -2675.185507
EM: Round [247] log likelihood: -2675.184936
EM: Round [248] log likelihood: -2675.184376
EM: Round [249] log likelihood: -2675.183826
EM: Round [250] log likelihood: -2675.183287
EM: Round [251] log likelihood: -2675.182758
EM: Round [252] log likelihood: -2675.182239
EM: Round [253] log likelihood: -2675.181730
EM: Round [254] log likelihood: -2675.181231
EM: Round [255] log likelihood: -2675.180741
EM: Round [256] log likelihood: -2675.180260
EM: Round [257] log likelihood: -2675.179788
EM: Round [258] log likelihood: -2675.179326
EM: Round [259] log likelihood: -2675.178872
EM: Round [260] log likelihood: -2675.178426
EM: Round [261] log likelihood: -2675.177989
EM: Round [262] log likelihood: -2675.177560
EM: Round [263] log likelihood: -2675.177140
EM: Round [264] log likelihood: -2675.176727
EM: Round [265] log likelihood: -2675.176322
EM: Round [266] log likelihood: -2675.175925
EM: Round [267] log likelihood: -2675.175535
EM: Round [268] log likelihood: -2675.175153
EM: Round [269] log likelihood: -2675.174778
EM: Round [270] log likelihood: -2675.174410
EM: Round [271] log likelihood: -2675.174049
EM: Round [272] log likelihood: -2675.173695
EM: Round [273] log likelihood: -2675.173347
EM: Round [274] log likelihood: -2675.173006
EM: Round [275] log likelihood: -2675.172672
EM: Round [276] log likelihood: -2675.172343
EM: Round [277] log likelihood: -2675.172021
EM: Round [278] log likelihood: -2675.171706
EM: Round [279] log likelihood: -2675.171396
EM: Round [280] log likelihood: -2675.171092
EM: Round [281] log likelihood: -2675.170793
EM: Round [282] log likelihood: -2675.170501
EM: Round [283] log likelihood: -2675.170213
EM: Round [284] log likelihood: -2675.169932
EM: Round [285] log likelihood: -2675.169655
EM: Round [286] log likelihood: -2675.169384
EM: Round [287] log likelihood: -2675.169118
EM: Round [288] log likelihood: -2675.168857
EM: Round [289] log likelihood: -2675.168601
EM: Round [290] log likelihood: -2675.168350
EM: Round [291] log likelihood: -2675.168103
EM: Round [292] log likelihood: -2675.167861
EM: Round [293] log likelihood: -2675.167624
EM: Round [294] log likelihood: -2675.167391
EM: Round [295] log likelihood: -2675.167163
EM: Round [296] log likelihood: -2675.166938
EM: Round [297] log likelihood: -2675.166719
EM: Round [298] log likelihood: -2675.166503
EM: Round [299] log likelihood: -2675.166291
EM: Round [300] log likelihood: -2675.166084
EM: Round [301] log likelihood: -2675.165880
EM: Round [302] log likelihood: -2675.165680
EM: Round [303] log likelihood: -2675.165484
EM: Round [304] log likelihood: -2675.165292
EM: Round [305] log likelihood: -2675.165103
EM: Round [306] log likelihood: -2675.164918
EM: Round [307] log likelihood: -2675.164736
EM: Round [308] log likelihood: -2675.164558
EM: Round [309] log likelihood: -2675.164383
EM: Round [310] log likelihood: -2675.164211
EM: Round [311] log likelihood: -2675.164043
EM: Round [312] log likelihood: -2675.163878
EM: Round [313] log likelihood: -2675.163716
EM: Round [314] log likelihood: -2675.163557
EM: Round [315] log likelihood: -2675.163401
EM: Round [316] log likelihood: -2675.163247
EM: Round [317] log likelihood: -2675.163097
EM: Round [318] log likelihood: -2675.162950
EM: Round [319] log likelihood: -2675.162805
EM: Round [320] log likelihood: -2675.162664
EM: Round [321] log likelihood: -2675.162524
EM: Round [322] log likelihood: -2675.162388
EM: Round [323] log likelihood: -2675.162254
EM: Round [324] log likelihood: -2675.162123
EM: Round [325] log likelihood: -2675.161994
EM: Round [326] log likelihood: -2675.161867
EM: Round [327] log likelihood: -2675.161743
EM: Round [328] log likelihood: -2675.161621
EM: Round [329] log likelihood: -2675.161502
EM: Round [330] log likelihood: -2675.161385
EM: Round [331] log likelihood: -2675.161270
EM: Round [332] log likelihood: -2675.161157
EM: Round [333] log likelihood: -2675.161046
EM: Round [334] log likelihood: -2675.160938
EM: Round [335] log likelihood: -2675.160831
EM: Round [336] log likelihood: -2675.160727
EM: Round [337] log likelihood: -2675.160624
EM: Round [338] log likelihood: -2675.160523
EM: Round [339] log likelihood: -2675.160425
EM: Stopping iterations at round 339 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.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam || : 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam || : 
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/tih_rna_sample_00467_B23WHTKLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.29 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.Pfam.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.Pfam.gff3 
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.seqsimilar.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa > /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.1wx8ERHk48/fi_workdir/tih_rna_sample_00467_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir
-done, see /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1390.592774
EM: Round [1] log likelihood: -1390.592774
EM: Stopping iterations at round 1 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.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2_1.fastp.fastq.gz: 295150503
Execution Time = 5.46 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa --gtf /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf  > /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fa --gtf /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gtf  > /tmp/nxf.1wx8ERHk48/fi_workdir/microH.dat
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.1wx8ERHk48/fi_workdir/microH.dat /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.1wx8ERHk48/fi_workdir/microH.dat /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.1wx8ERHk48 --json_outfile /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00467_B23WHTKLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.1wx8ERHk48 --json_outfile /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00467_B23WHTKLT4_2
Running: touch /tmp/nxf.1wx8ERHk48/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.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00467_B23WHTKLT4_2 --html_output /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00467_B23WHTKLT4_2 --html_output /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000248515.2]
WARNING, no entry stored in dbm for [ENSG00000248515.2]
WARNING, no entry stored in dbm for [ENSG00000248515.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.1wx8ERHk48/ctat_genome_lib_build_dir > /tmp/nxf.1wx8ERHk48/tih_rna_sample_00467_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.1wx8ERHk48/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory