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/90/b9df2224558dabc4b58dc2a752d41a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/f1a140e26752d178425115b4293a36/659_bR4-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/f1a140e26752d178425115b4293a36/659_bR4-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/b9df2224558dabc4b58dc2a752d41a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/961b0a4a1525e6a2079c05d0e80110/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.23 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.LnHg90Bm8f/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.LnHg90Bm8f/cytoBand.txt
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bR4-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.LnHg90Bm8f/fi_workdir --reads "/tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.LnHg90Bm8f/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.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 04 22:14:53 ..... started STAR run
Jun 04 22:14:53 ..... loading genome
Jun 04 22:17:37 ... generating Suffix Array index
Jun 04 22:24:25 ... completed Suffix Array index
Jun 04 22:24:25 ..... processing annotations GTF
Jun 04 22:24:26 ..... inserting junctions into the genome indices
Jun 04 22:26:04 ..... started mapping
Jun 04 23:20:05 ..... finished mapping
Jun 04 23:20:08 ..... started sorting BAM
Jun 04 23:20:09 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 65.32 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bR4-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.LnHg90Bm8f/fi_workdir --reads "/tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
23:20:29 : INFO : Done.
Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.LnHg90Bm8f/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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[3200000]   -done parsing /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 22,
          'low complexity anchor region' => 15,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 20,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 3,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 250,
          'small anchor length' => 103,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
          'seq-similar region overlap' => 321,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 24,
          ' ** passed ** ' => 11163,
          'per_id < 96' => 11612,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 96,
          'num genes matched < 2' => 268,
          'excessive soft clipping' => 19939,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9
        };
-writing fusion junction support info.
Execution Time = 1.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.LnHg90Bm8f/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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   -fusion SPANNING read extraction for scaff: AC007785.3--IGFL2

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[16000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

[1000]   -fusion SPANNING read extraction for scaff: AC217774.1--CRHR1

[1000]   -fusion SPANNING read extraction for scaff: AC217774.2--CRHR1

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[26000]   -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180

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[167000]   -fusion SPANNING read extraction for scaff: ATP11A--STK26

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[179000]   -fusion SPANNING read extraction for scaff: BCL2--ZNF521

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[87000]   -fusion SPANNING read extraction for scaff: DOCK9--SERPINE2

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[60000]   -fusion SPANNING read extraction for scaff: DTNB--SERPINE2

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[38000]   
[39000]   -fusion SPANNING read extraction for scaff: DTNB--USP21P1

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[278000]   -fusion SPANNING read extraction for scaff: EML4--ALK

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[23000]   -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1

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[42000]   -fusion SPANNING read extraction for scaff: GFPT1--ENOX2

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[6000]   -fusion SPANNING read extraction for scaff: IGFL1P2--HIF3A

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[104000]   -fusion SPANNING read extraction for scaff: KDM3A--TOP1

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[629000]   
[630000]   -fusion SPANNING read extraction for scaff: KDM5C--KMT2C

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: LINC01654--IGSF21

[1000]   -fusion SPANNING read extraction for scaff: LINC02210--CRHR1

[1000]   
[2000]   
[3000]   
[4000]   -fusion SPANNING read extraction for scaff: LRCH2--SPANXN1

[1000]   
[2000]   
[3000]   
[4000]   -fusion SPANNING read extraction for scaff: LRCH2--TRMT1P1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[55000]   
[56000]   
[57000]   -fusion SPANNING read extraction for scaff: MED14--PRRG1

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   -fusion SPANNING read extraction for scaff: MED14--FTH1P19

[1000]   
[2000]   
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[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
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[50000]   
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[54000]   
[55000]   
[56000]   -fusion SPANNING read extraction for scaff: MED14--FTH1P27

[1000]   
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[250000]   
[251000]   -fusion SPANNING read extraction for scaff: MGAT4A--SNRNP200

[1000]   
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[6000]   
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[8000]   
[9000]   
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[89000]   -fusion SPANNING read extraction for scaff: MRPS21--APH1A

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[11000]   -fusion SPANNING read extraction for scaff: ORC2--AC068196.1

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[48000]   -fusion SPANNING read extraction for scaff: PARP8--LINC00276

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA8

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA9

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGB6

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA10

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[6000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGB7

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA11

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA12

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[20000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC3

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC4

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[6000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC5

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PLCL1--GULP1

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[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146

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[42000]   
[43000]   -fusion SPANNING read extraction for scaff: PPP1R13B--ZNF138

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[66000]   
[67000]   -fusion SPANNING read extraction for scaff: R3HDM1--RNF144A

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[55000]   
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[65000]   
[66000]   
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[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   -fusion SPANNING read extraction for scaff: RMND5A--KDM3A

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[8000]   
[9000]   
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[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: RNF144A--AC068725.1

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[8000]   
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[13000]   
[14000]   
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[20000]   
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[30000]   
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[33000]   
[34000]   
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[40000]   
[41000]   
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[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   -fusion SPANNING read extraction for scaff: ROCK2--ZNF385B

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[8000]   
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[14000]   
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[20000]   
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[25000]   
[26000]   
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[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   -fusion SPANNING read extraction for scaff: RUNDC3B--ADAM22

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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: SLC25A12--AC092623.1

[1000]   
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[6000]   
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[8000]   
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[30000]   
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[32000]   
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[34000]   
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[39000]   
[40000]   
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[48000]   
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[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   -fusion SPANNING read extraction for scaff: SLC25A12--MGAT5

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[100000]   
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[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   -fusion SPANNING read extraction for scaff: SLFN11--SLFN12

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[41000]   
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[60000]   
[61000]   
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[64000]   
[65000]   
[66000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[8000]   
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[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: TDRD9--ZNF107

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[36000]   
[37000]   
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[40000]   
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[43000]   
[44000]   
[45000]   -fusion SPANNING read extraction for scaff: TLK2--AL669831.1

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[11000]   
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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[8000]   
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[20000]   
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[27000]   
[28000]   -fusion SPANNING read extraction for scaff: TYW1--ZNF138

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[64000]   
[65000]   
[66000]   -fusion SPANNING read extraction for scaff: ZNF521--RN7SL97P

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[20000]   
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[24000]   
[25000]   
[26000]   
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[29000]   
[30000]   
[31000]   
[32000]   -fusion SPANNING read extraction for scaff: ZNF680--TMEM248

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[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: ZNF92--TDRD9

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[7000]   
[8000]   -fusion SPANNING read extraction for scaff: ZNF92--RNU6-1254P

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[7000]   
[8000]   -fusion SPANNING read extraction for scaff: ZNF92--LINC02604
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 37138,
          'lacks exon overlap' => 10687
        };
Execution Time = 4.98 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.LnHg90Bm8f/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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -14726.174202
EM: Round [1] log likelihood: -14722.493117
EM: Round [2] log likelihood: -14720.792002
EM: Round [3] log likelihood: -14719.400181
EM: Round [4] log likelihood: -14718.249661
EM: Round [5] log likelihood: -14717.291713
EM: Round [6] log likelihood: -14716.489467
EM: Round [7] log likelihood: -14715.814441
EM: Round [8] log likelihood: -14715.244262
EM: Round [9] log likelihood: -14714.761103
EM: Round [10] log likelihood: -14714.350593
EM: Round [11] log likelihood: -14714.001030
EM: Round [12] log likelihood: -14713.702809
EM: Round [13] log likelihood: -14713.447987
EM: Round [14] log likelihood: -14713.229957
EM: Round [15] log likelihood: -14713.043196
EM: Round [16] log likelihood: -14712.883064
EM: Round [17] log likelihood: -14712.745651
EM: Round [18] log likelihood: -14712.627652
EM: Round [19] log likelihood: -14712.526263
EM: Round [20] log likelihood: -14712.439101
EM: Round [21] log likelihood: -14712.364136
EM: Round [22] log likelihood: -14712.299638
EM: Round [23] log likelihood: -14712.244126
EM: Round [24] log likelihood: -14712.196337
EM: Round [25] log likelihood: -14712.155184
EM: Round [26] log likelihood: -14712.119741
EM: Round [27] log likelihood: -14712.089208
EM: Round [28] log likelihood: -14712.062902
EM: Round [29] log likelihood: -14712.040235
EM: Round [30] log likelihood: -14712.020701
EM: Round [31] log likelihood: -14712.003865
EM: Round [32] log likelihood: -14711.989354
EM: Round [33] log likelihood: -14711.976845
EM: Round [34] log likelihood: -14711.966062
EM: Round [35] log likelihood: -14711.956765
EM: Round [36] log likelihood: -14711.948751
EM: Round [37] log likelihood: -14711.941841
EM: Round [38] log likelihood: -14711.935883
EM: Round [39] log likelihood: -14711.930746
EM: Round [40] log likelihood: -14711.926317
EM: Round [41] log likelihood: -14711.922498
EM: Round [42] log likelihood: -14711.919205
EM: Round [43] log likelihood: -14711.916365
EM: Round [44] log likelihood: -14711.913916
EM: Round [45] log likelihood: -14711.911804
EM: Round [46] log likelihood: -14711.909984
EM: Round [47] log likelihood: -14711.908413
EM: Round [48] log likelihood: -14711.907059
EM: Round [49] log likelihood: -14711.905892
EM: Round [50] log likelihood: -14711.904885
EM: Round [51] log likelihood: -14711.904016
EM: Round [52] log likelihood: -14711.903267
EM: Round [53] log likelihood: -14711.902622
EM: Round [54] log likelihood: -14711.902065
EM: Round [55] log likelihood: -14711.901584
EM: Round [56] log likelihood: -14711.901170
EM: Round [57] log likelihood: -14711.900813
EM: Round [58] log likelihood: -14711.900505
EM: Round [59] log likelihood: -14711.900240
EM: Round [60] log likelihood: -14711.900010
EM: Round [61] log likelihood: -14711.899813
EM: Round [62] log likelihood: -14711.899643
EM: Round [63] log likelihood: -14711.899496
EM: Round [64] log likelihood: -14711.899369
EM: Round [65] log likelihood: -14711.899260
EM: Round [66] log likelihood: -14711.899165
EM: Stopping iterations at round 66 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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.LnHg90Bm8f/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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.LnHg90Bm8f/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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.LnHg90Bm8f/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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.LnHg90Bm8f/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.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.LnHg90Bm8f/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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir
-done, see /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -14396.958302
EM: Round [1] log likelihood: -14396.288098
EM: Round [2] log likelihood: -14396.287151
EM: Round [3] log likelihood: -14396.287149
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 290821167
Execution Time = 5.65 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.LnHg90Bm8f/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.LnHg90Bm8f/fi_workdir/microH.dat
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.LnHg90Bm8f/fi_workdir/microH.dat /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_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.LnHg90Bm8f/fi_workdir/microH.dat /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.LnHg90Bm8f --json_outfile /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bR4-T1-TRNA-1_B23MHV2LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.LnHg90Bm8f --json_outfile /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bR4-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.LnHg90Bm8f/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.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bR4-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 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.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bR4-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
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 [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 [ENSG00000285548.1]
WARNING, no entry stored in dbm for [ENSG00000285548.1]
WARNING, no entry stored in dbm for [ENSG00000285548.1]
WARNING, no entry stored in dbm for [ENSG00000285548.1]
WARNING, no entry stored in dbm for [ENSG00000268401.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000204650.14]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.LnHg90Bm8f/ctat_genome_lib_build_dir > /tmp/nxf.LnHg90Bm8f/659_bR4-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.LnHg90Bm8f/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory