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/b9/aaf3ee6440e03466793c61c0189e9f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/8115a6cc2c2b27fee8798083f699bf/659_bGc-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/f2fe8554f6b3f349cdcffa1aed284b/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/aaf3ee6440e03466793c61c0189e9f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/8115a6cc2c2b27fee8798083f699bf/659_bGc-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.OFF5IVX0JR/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.OFF5IVX0JR/cytoBand.txt
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bGc-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.OFF5IVX0JR/fi_workdir --reads "/tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:45:21 ..... started STAR run
Jun 08 09:45:21 ..... loading genome
Jun 08 09:47:05 ... generating Suffix Array index
Jun 08 09:51:57 ... completed Suffix Array index
Jun 08 09:51:57 ..... processing annotations GTF
Jun 08 09:51:57 ..... inserting junctions into the genome indices
Jun 08 09:52:59 ..... started mapping
Jun 08 10:49:30 ..... finished mapping
Jun 08 10:49:32 ..... started sorting BAM
Jun 08 10:49:33 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 64.23 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bGc-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.OFF5IVX0JR/fi_workdir --reads "/tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
10:49:45 : INFO : Done.
Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[1870000]   -done parsing /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-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 2 ' => 290,
          'small anchor length' => 65,
          'low complexity anchor region' => 10,
          'per_id < 96' => 6993,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2,
          'exons hit < 2' => 3,
          'num genes matched < 2' => 21,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 50,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 251,
          'excessive soft clipping' => 10796,
          'seq-similar region overlap' => 80,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          ' ** passed ** ' => 12422,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 18
        };
-writing fusion junction support info.
Execution Time = 1.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[404000]   -fusion SPANNING read extraction for scaff: KIF5B--RET

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

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[851000]   -fusion SPANNING read extraction for scaff: NOTCH2--NBPF11

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8

[1000]   
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[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10

[1000]   
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[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5

[1000]   
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[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6

[1000]   
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[4000]   
[5000]   
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[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9

[1000]   
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[9000]   
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[11000]   
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[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7

[1000]   
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[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12

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[66000]   
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[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3

[1000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
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[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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

[1000]   
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[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
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[3000]   
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[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
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[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
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[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
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[14000]   
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[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
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[30000]   
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[38000]   
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[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
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[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
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[8000]   
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[14000]   
[15000]   
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[20000]   
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[25000]   
[26000]   
[27000]   
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[29000]   
[30000]   
[31000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
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[67000]   
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[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   -fusion SPANNING read extraction for scaff: PTMS--MTRNR2L8

[1000]   
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[8000]   
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[41000]   
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[46000]   
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[63000]   
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[65000]   
[66000]   
[67000]   
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[69000]   
[70000]   
[71000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[8000]   
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[27000]   
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[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: TLK2--LINC01002

[1000]   
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[25000]   
[26000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 4444,
          'seq similar region alignment' => 21269
        };
Execution Time = 3.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4814.386721
EM: Round [1] log likelihood: -4813.196077
EM: Round [2] log likelihood: -4812.174520
EM: Round [3] log likelihood: -4811.255063
EM: Round [4] log likelihood: -4810.416783
EM: Round [5] log likelihood: -4809.645371
EM: Round [6] log likelihood: -4808.930738
EM: Round [7] log likelihood: -4808.265562
EM: Round [8] log likelihood: -4807.644356
EM: Round [9] log likelihood: -4807.062865
EM: Round [10] log likelihood: -4806.517660
EM: Round [11] log likelihood: -4806.005878
EM: Round [12] log likelihood: -4805.525043
EM: Round [13] log likelihood: -4805.072952
EM: Round [14] log likelihood: -4804.647604
EM: Round [15] log likelihood: -4804.247155
EM: Round [16] log likelihood: -4803.869887
EM: Round [17] log likelihood: -4803.514194
EM: Round [18] log likelihood: -4803.178573
EM: Round [19] log likelihood: -4802.861615
EM: Round [20] log likelihood: -4802.562002
EM: Round [21] log likelihood: -4802.278504
EM: Round [22] log likelihood: -4802.009978
EM: Round [23] log likelihood: -4801.755361
EM: Round [24] log likelihood: -4801.513669
EM: Round [25] log likelihood: -4801.283993
EM: Round [26] log likelihood: -4801.065493
EM: Round [27] log likelihood: -4800.857398
EM: Round [28] log likelihood: -4800.658997
EM: Round [29] log likelihood: -4800.469637
EM: Round [30] log likelihood: -4800.288719
EM: Round [31] log likelihood: -4800.115692
EM: Round [32] log likelihood: -4799.950053
EM: Round [33] log likelihood: -4799.791337
EM: Round [34] log likelihood: -4799.639119
EM: Round [35] log likelihood: -4799.493009
EM: Round [36] log likelihood: -4799.352647
EM: Round [37] log likelihood: -4799.217703
EM: Round [38] log likelihood: -4799.087873
EM: Round [39] log likelihood: -4798.962875
EM: Round [40] log likelihood: -4798.842451
EM: Round [41] log likelihood: -4798.726360
EM: Round [42] log likelihood: -4798.614382
EM: Round [43] log likelihood: -4798.506309
EM: Round [44] log likelihood: -4798.401951
EM: Round [45] log likelihood: -4798.301131
EM: Round [46] log likelihood: -4798.203682
EM: Round [47] log likelihood: -4798.109449
EM: Round [48] log likelihood: -4798.018289
EM: Round [49] log likelihood: -4797.930066
EM: Round [50] log likelihood: -4797.844652
EM: Round [51] log likelihood: -4797.761930
EM: Round [52] log likelihood: -4797.681787
EM: Round [53] log likelihood: -4797.604117
EM: Round [54] log likelihood: -4797.528821
EM: Round [55] log likelihood: -4797.455806
EM: Round [56] log likelihood: -4797.384982
EM: Round [57] log likelihood: -4797.316265
EM: Round [58] log likelihood: -4797.249576
EM: Round [59] log likelihood: -4797.184840
EM: Round [60] log likelihood: -4797.121984
EM: Round [61] log likelihood: -4797.060940
EM: Round [62] log likelihood: -4797.001644
EM: Round [63] log likelihood: -4796.944033
EM: Round [64] log likelihood: -4796.888050
EM: Round [65] log likelihood: -4796.833636
EM: Round [66] log likelihood: -4796.780740
EM: Round [67] log likelihood: -4796.729309
EM: Round [68] log likelihood: -4796.679295
EM: Round [69] log likelihood: -4796.630650
EM: Round [70] log likelihood: -4796.583330
EM: Round [71] log likelihood: -4796.537291
EM: Round [72] log likelihood: -4796.492493
EM: Round [73] log likelihood: -4796.448895
EM: Round [74] log likelihood: -4796.406460
EM: Round [75] log likelihood: -4796.365151
EM: Round [76] log likelihood: -4796.324933
EM: Round [77] log likelihood: -4796.285772
EM: Round [78] log likelihood: -4796.247636
EM: Round [79] log likelihood: -4796.210493
EM: Round [80] log likelihood: -4796.174314
EM: Round [81] log likelihood: -4796.139070
EM: Round [82] log likelihood: -4796.104733
EM: Round [83] log likelihood: -4796.071275
EM: Round [84] log likelihood: -4796.038672
EM: Round [85] log likelihood: -4796.006897
EM: Round [86] log likelihood: -4795.975928
EM: Round [87] log likelihood: -4795.945740
EM: Round [88] log likelihood: -4795.916311
EM: Round [89] log likelihood: -4795.887620
EM: Round [90] log likelihood: -4795.859645
EM: Round [91] log likelihood: -4795.832367
EM: Round [92] log likelihood: -4795.805766
EM: Round [93] log likelihood: -4795.779822
EM: Round [94] log likelihood: -4795.754518
EM: Round [95] log likelihood: -4795.729836
EM: Round [96] log likelihood: -4795.705759
EM: Round [97] log likelihood: -4795.682270
EM: Round [98] log likelihood: -4795.659353
EM: Round [99] log likelihood: -4795.636993
EM: Round [100] log likelihood: -4795.615174
EM: Round [101] log likelihood: -4795.593883
EM: Round [102] log likelihood: -4795.573104
EM: Round [103] log likelihood: -4795.552825
EM: Round [104] log likelihood: -4795.533031
EM: Round [105] log likelihood: -4795.513711
EM: Round [106] log likelihood: -4795.494852
EM: Round [107] log likelihood: -4795.476441
EM: Round [108] log likelihood: -4795.458467
EM: Round [109] log likelihood: -4795.440918
EM: Round [110] log likelihood: -4795.423784
EM: Round [111] log likelihood: -4795.407054
EM: Round [112] log likelihood: -4795.390717
EM: Round [113] log likelihood: -4795.374763
EM: Round [114] log likelihood: -4795.359183
EM: Round [115] log likelihood: -4795.343966
EM: Round [116] log likelihood: -4795.329105
EM: Round [117] log likelihood: -4795.314589
EM: Round [118] log likelihood: -4795.300409
EM: Round [119] log likelihood: -4795.286559
EM: Round [120] log likelihood: -4795.273028
EM: Round [121] log likelihood: -4795.259810
EM: Round [122] log likelihood: -4795.246896
EM: Round [123] log likelihood: -4795.234280
EM: Round [124] log likelihood: -4795.221952
EM: Round [125] log likelihood: -4795.209907
EM: Round [126] log likelihood: -4795.198137
EM: Round [127] log likelihood: -4795.186636
EM: Round [128] log likelihood: -4795.175397
EM: Round [129] log likelihood: -4795.164414
EM: Round [130] log likelihood: -4795.153680
EM: Round [131] log likelihood: -4795.143189
EM: Round [132] log likelihood: -4795.132935
EM: Round [133] log likelihood: -4795.122913
EM: Round [134] log likelihood: -4795.113118
EM: Round [135] log likelihood: -4795.103542
EM: Round [136] log likelihood: -4795.094182
EM: Round [137] log likelihood: -4795.085033
EM: Round [138] log likelihood: -4795.076088
EM: Round [139] log likelihood: -4795.067343
EM: Round [140] log likelihood: -4795.058794
EM: Round [141] log likelihood: -4795.050435
EM: Round [142] log likelihood: -4795.042263
EM: Round [143] log likelihood: -4795.034273
EM: Round [144] log likelihood: -4795.026460
EM: Round [145] log likelihood: -4795.018820
EM: Round [146] log likelihood: -4795.011350
EM: Round [147] log likelihood: -4795.004045
EM: Round [148] log likelihood: -4794.996901
EM: Round [149] log likelihood: -4794.989915
EM: Round [150] log likelihood: -4794.983083
EM: Round [151] log likelihood: -4794.976401
EM: Round [152] log likelihood: -4794.969866
EM: Round [153] log likelihood: -4794.963475
EM: Round [154] log likelihood: -4794.957223
EM: Round [155] log likelihood: -4794.951109
EM: Round [156] log likelihood: -4794.945128
EM: Round [157] log likelihood: -4794.939277
EM: Round [158] log likelihood: -4794.933555
EM: Round [159] log likelihood: -4794.927957
EM: Round [160] log likelihood: -4794.922481
EM: Round [161] log likelihood: -4794.917123
EM: Round [162] log likelihood: -4794.911882
EM: Round [163] log likelihood: -4794.906755
EM: Round [164] log likelihood: -4794.901739
EM: Round [165] log likelihood: -4794.896831
EM: Round [166] log likelihood: -4794.892029
EM: Round [167] log likelihood: -4794.887331
EM: Round [168] log likelihood: -4794.882735
EM: Round [169] log likelihood: -4794.878237
EM: Round [170] log likelihood: -4794.873836
EM: Round [171] log likelihood: -4794.869529
EM: Round [172] log likelihood: -4794.865315
EM: Round [173] log likelihood: -4794.861191
EM: Round [174] log likelihood: -4794.857156
EM: Round [175] log likelihood: -4794.853207
EM: Round [176] log likelihood: -4794.849342
EM: Round [177] log likelihood: -4794.845560
EM: Round [178] log likelihood: -4794.841859
EM: Round [179] log likelihood: -4794.838236
EM: Round [180] log likelihood: -4794.834691
EM: Round [181] log likelihood: -4794.831221
EM: Round [182] log likelihood: -4794.827824
EM: Round [183] log likelihood: -4794.824500
EM: Round [184] log likelihood: -4794.821246
EM: Round [185] log likelihood: -4794.818061
EM: Round [186] log likelihood: -4794.814944
EM: Round [187] log likelihood: -4794.811892
EM: Round [188] log likelihood: -4794.808905
EM: Round [189] log likelihood: -4794.805981
EM: Round [190] log likelihood: -4794.803118
EM: Round [191] log likelihood: -4794.800316
EM: Round [192] log likelihood: -4794.797573
EM: Round [193] log likelihood: -4794.794887
EM: Round [194] log likelihood: -4794.792258
EM: Round [195] log likelihood: -4794.789684
EM: Round [196] log likelihood: -4794.787164
EM: Round [197] log likelihood: -4794.784696
EM: Round [198] log likelihood: -4794.782281
EM: Round [199] log likelihood: -4794.779915
EM: Round [200] log likelihood: -4794.777600
EM: Round [201] log likelihood: -4794.775332
EM: Round [202] log likelihood: -4794.773112
EM: Round [203] log likelihood: -4794.770938
EM: Round [204] log likelihood: -4794.768809
EM: Round [205] log likelihood: -4794.766725
EM: Round [206] log likelihood: -4794.764684
EM: Round [207] log likelihood: -4794.762685
EM: Round [208] log likelihood: -4794.760728
EM: Round [209] log likelihood: -4794.758811
EM: Round [210] log likelihood: -4794.756934
EM: Round [211] log likelihood: -4794.755096
EM: Round [212] log likelihood: -4794.753296
EM: Round [213] log likelihood: -4794.751533
EM: Round [214] log likelihood: -4794.749806
EM: Round [215] log likelihood: -4794.748115
EM: Round [216] log likelihood: -4794.746459
EM: Round [217] log likelihood: -4794.744837
EM: Round [218] log likelihood: -4794.743248
EM: Round [219] log likelihood: -4794.741692
EM: Round [220] log likelihood: -4794.740168
EM: Round [221] log likelihood: -4794.738675
EM: Round [222] log likelihood: -4794.737213
EM: Round [223] log likelihood: -4794.735781
EM: Round [224] log likelihood: -4794.734378
EM: Round [225] log likelihood: -4794.733004
EM: Round [226] log likelihood: -4794.731658
EM: Round [227] log likelihood: -4794.730339
EM: Round [228] log likelihood: -4794.729048
EM: Round [229] log likelihood: -4794.727782
EM: Round [230] log likelihood: -4794.726543
EM: Round [231] log likelihood: -4794.725328
EM: Round [232] log likelihood: -4794.724139
EM: Round [233] log likelihood: -4794.722973
EM: Round [234] log likelihood: -4794.721832
EM: Round [235] log likelihood: -4794.720713
EM: Round [236] log likelihood: -4794.719617
EM: Round [237] log likelihood: -4794.718544
EM: Round [238] log likelihood: -4794.717492
EM: Round [239] log likelihood: -4794.716461
EM: Round [240] log likelihood: -4794.715452
EM: Round [241] log likelihood: -4794.714463
EM: Round [242] log likelihood: -4794.713493
EM: Round [243] log likelihood: -4794.712544
EM: Round [244] log likelihood: -4794.711613
EM: Round [245] log likelihood: -4794.710701
EM: Round [246] log likelihood: -4794.709808
EM: Round [247] log likelihood: -4794.708932
EM: Round [248] log likelihood: -4794.708074
EM: Round [249] log likelihood: -4794.707234
EM: Round [250] log likelihood: -4794.706410
EM: Round [251] log likelihood: -4794.705603
EM: Round [252] log likelihood: -4794.704812
EM: Round [253] log likelihood: -4794.704037
EM: Round [254] log likelihood: -4794.703277
EM: Round [255] log likelihood: -4794.702533
EM: Round [256] log likelihood: -4794.701804
EM: Round [257] log likelihood: -4794.701089
EM: Round [258] log likelihood: -4794.700388
EM: Round [259] log likelihood: -4794.699702
EM: Round [260] log likelihood: -4794.699029
EM: Round [261] log likelihood: -4794.698369
EM: Round [262] log likelihood: -4794.697723
EM: Round [263] log likelihood: -4794.697090
EM: Round [264] log likelihood: -4794.696469
EM: Round [265] log likelihood: -4794.695860
EM: Round [266] log likelihood: -4794.695264
EM: Round [267] log likelihood: -4794.694679
EM: Round [268] log likelihood: -4794.694106
EM: Round [269] log likelihood: -4794.693545
EM: Round [270] log likelihood: -4794.692994
EM: Round [271] log likelihood: -4794.692455
EM: Round [272] log likelihood: -4794.691926
EM: Round [273] log likelihood: -4794.691408
EM: Round [274] log likelihood: -4794.690899
EM: Round [275] log likelihood: -4794.690401
EM: Round [276] log likelihood: -4794.689913
EM: Round [277] log likelihood: -4794.689435
EM: Round [278] log likelihood: -4794.688965
EM: Round [279] log likelihood: -4794.688506
EM: Round [280] log likelihood: -4794.688055
EM: Round [281] log likelihood: -4794.687613
EM: Round [282] log likelihood: -4794.687180
EM: Round [283] log likelihood: -4794.686755
EM: Round [284] log likelihood: -4794.686338
EM: Round [285] log likelihood: -4794.685930
EM: Round [286] log likelihood: -4794.685530
EM: Round [287] log likelihood: -4794.685138
EM: Round [288] log likelihood: -4794.684753
EM: Round [289] log likelihood: -4794.684376
EM: Round [290] log likelihood: -4794.684006
EM: Round [291] log likelihood: -4794.683644
EM: Round [292] log likelihood: -4794.683289
EM: Round [293] log likelihood: -4794.682940
EM: Round [294] log likelihood: -4794.682599
EM: Round [295] log likelihood: -4794.682264
EM: Round [296] log likelihood: -4794.681935
EM: Round [297] log likelihood: -4794.681613
EM: Round [298] log likelihood: -4794.681298
EM: Round [299] log likelihood: -4794.680988
EM: Round [300] log likelihood: -4794.680685
EM: Round [301] log likelihood: -4794.680387
EM: Round [302] log likelihood: -4794.680095
EM: Round [303] log likelihood: -4794.679809
EM: Round [304] log likelihood: -4794.679528
EM: Round [305] log likelihood: -4794.679253
EM: Round [306] log likelihood: -4794.678984
EM: Round [307] log likelihood: -4794.678719
EM: Round [308] log likelihood: -4794.678460
EM: Round [309] log likelihood: -4794.678205
EM: Round [310] log likelihood: -4794.677956
EM: Round [311] log likelihood: -4794.677711
EM: Round [312] log likelihood: -4794.677471
EM: Round [313] log likelihood: -4794.677236
EM: Round [314] log likelihood: -4794.677005
EM: Round [315] log likelihood: -4794.676779
EM: Round [316] log likelihood: -4794.676557
EM: Round [317] log likelihood: -4794.676340
EM: Round [318] log likelihood: -4794.676126
EM: Round [319] log likelihood: -4794.675917
EM: Round [320] log likelihood: -4794.675712
EM: Round [321] log likelihood: -4794.675511
EM: Round [322] log likelihood: -4794.675313
EM: Round [323] log likelihood: -4794.675120
EM: Round [324] log likelihood: -4794.674930
EM: Round [325] log likelihood: -4794.674744
EM: Round [326] log likelihood: -4794.674561
EM: Round [327] log likelihood: -4794.674382
EM: Round [328] log likelihood: -4794.674206
EM: Round [329] log likelihood: -4794.674034
EM: Round [330] log likelihood: -4794.673865
EM: Round [331] log likelihood: -4794.673699
EM: Round [332] log likelihood: -4794.673537
EM: Round [333] log likelihood: -4794.673377
EM: Round [334] log likelihood: -4794.673221
EM: Round [335] log likelihood: -4794.673067
EM: Round [336] log likelihood: -4794.672917
EM: Round [337] log likelihood: -4794.672769
EM: Round [338] log likelihood: -4794.672625
EM: Round [339] log likelihood: -4794.672483
EM: Round [340] log likelihood: -4794.672343
EM: Round [341] log likelihood: -4794.672207
EM: Round [342] log likelihood: -4794.672073
EM: Round [343] log likelihood: -4794.671941
EM: Round [344] log likelihood: -4794.671812
EM: Round [345] log likelihood: -4794.671686
EM: Round [346] log likelihood: -4794.671562
EM: Round [347] log likelihood: -4794.671440
EM: Round [348] log likelihood: -4794.671320
EM: Round [349] log likelihood: -4794.671203
EM: Round [350] log likelihood: -4794.671088
EM: Round [351] log likelihood: -4794.670976
EM: Round [352] log likelihood: -4794.670865
EM: Round [353] log likelihood: -4794.670757
EM: Round [354] log likelihood: -4794.670650
EM: Round [355] log likelihood: -4794.670546
EM: Round [356] log likelihood: -4794.670443
EM: Round [357] log likelihood: -4794.670343
EM: Round [358] log likelihood: -4794.670244
EM: Stopping iterations at round 358 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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.48 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/fi_workdir/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir
-done, see /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -3735.663628
EM: Round [1] log likelihood: -3735.551309
EM: Round [2] log likelihood: -3735.471221
EM: Round [3] log likelihood: -3735.394969
EM: Round [4] log likelihood: -3735.322330
EM: Round [5] log likelihood: -3735.253101
EM: Round [6] log likelihood: -3735.187093
EM: Round [7] log likelihood: -3735.124130
EM: Round [8] log likelihood: -3735.064050
EM: Round [9] log likelihood: -3735.006701
EM: Round [10] log likelihood: -3734.951940
EM: Round [11] log likelihood: -3734.899636
EM: Round [12] log likelihood: -3734.849664
EM: Round [13] log likelihood: -3734.801908
EM: Round [14] log likelihood: -3734.756259
EM: Round [15] log likelihood: -3734.712614
EM: Round [16] log likelihood: -3734.670878
EM: Round [17] log likelihood: -3734.630959
EM: Round [18] log likelihood: -3734.592772
EM: Round [19] log likelihood: -3734.556236
EM: Round [20] log likelihood: -3734.521275
EM: Round [21] log likelihood: -3734.487816
EM: Round [22] log likelihood: -3734.455792
EM: Round [23] log likelihood: -3734.425138
EM: Round [24] log likelihood: -3734.395792
EM: Round [25] log likelihood: -3734.367696
EM: Round [26] log likelihood: -3734.340796
EM: Round [27] log likelihood: -3734.315038
EM: Round [28] log likelihood: -3734.290373
EM: Round [29] log likelihood: -3734.266753
EM: Round [30] log likelihood: -3734.244134
EM: Round [31] log likelihood: -3734.222472
EM: Round [32] log likelihood: -3734.201726
EM: Round [33] log likelihood: -3734.181857
EM: Round [34] log likelihood: -3734.162828
EM: Round [35] log likelihood: -3734.144604
EM: Round [36] log likelihood: -3734.127151
EM: Round [37] log likelihood: -3734.110435
EM: Round [38] log likelihood: -3734.094426
EM: Round [39] log likelihood: -3734.079095
EM: Round [40] log likelihood: -3734.064413
EM: Round [41] log likelihood: -3734.050353
EM: Round [42] log likelihood: -3734.036889
EM: Round [43] log likelihood: -3734.023996
EM: Round [44] log likelihood: -3734.011651
EM: Round [45] log likelihood: -3733.999831
EM: Round [46] log likelihood: -3733.988514
EM: Round [47] log likelihood: -3733.977678
EM: Round [48] log likelihood: -3733.967306
EM: Round [49] log likelihood: -3733.957376
EM: Round [50] log likelihood: -3733.947871
EM: Round [51] log likelihood: -3733.938772
EM: Round [52] log likelihood: -3733.930064
EM: Round [53] log likelihood: -3733.921730
EM: Round [54] log likelihood: -3733.913755
EM: Round [55] log likelihood: -3733.906123
EM: Round [56] log likelihood: -3733.898820
EM: Round [57] log likelihood: -3733.891833
EM: Round [58] log likelihood: -3733.885148
EM: Round [59] log likelihood: -3733.878753
EM: Round [60] log likelihood: -3733.872636
EM: Round [61] log likelihood: -3733.866785
EM: Round [62] log likelihood: -3733.861189
EM: Round [63] log likelihood: -3733.855837
EM: Round [64] log likelihood: -3733.850719
EM: Round [65] log likelihood: -3733.845825
EM: Round [66] log likelihood: -3733.841147
EM: Round [67] log likelihood: -3733.836673
EM: Round [68] log likelihood: -3733.832397
EM: Round [69] log likelihood: -3733.828309
EM: Round [70] log likelihood: -3733.824402
EM: Round [71] log likelihood: -3733.820668
EM: Round [72] log likelihood: -3733.817100
EM: Round [73] log likelihood: -3733.813690
EM: Round [74] log likelihood: -3733.810432
EM: Round [75] log likelihood: -3733.807319
EM: Round [76] log likelihood: -3733.804346
EM: Round [77] log likelihood: -3733.801505
EM: Round [78] log likelihood: -3733.798791
EM: Round [79] log likelihood: -3733.796200
EM: Round [80] log likelihood: -3733.793725
EM: Round [81] log likelihood: -3733.791361
EM: Round [82] log likelihood: -3733.789104
EM: Round [83] log likelihood: -3733.786950
EM: Round [84] log likelihood: -3733.784892
EM: Round [85] log likelihood: -3733.782928
EM: Round [86] log likelihood: -3733.781054
EM: Round [87] log likelihood: -3733.779264
EM: Round [88] log likelihood: -3733.777556
EM: Round [89] log likelihood: -3733.775926
EM: Round [90] log likelihood: -3733.774371
EM: Round [91] log likelihood: -3733.772887
EM: Round [92] log likelihood: -3733.771471
EM: Round [93] log likelihood: -3733.770120
EM: Round [94] log likelihood: -3733.768831
EM: Round [95] log likelihood: -3733.767601
EM: Round [96] log likelihood: -3733.766428
EM: Round [97] log likelihood: -3733.765310
EM: Round [98] log likelihood: -3733.764243
EM: Round [99] log likelihood: -3733.763225
EM: Round [100] log likelihood: -3733.762255
EM: Round [101] log likelihood: -3733.761330
EM: Round [102] log likelihood: -3733.760448
EM: Round [103] log likelihood: -3733.759606
EM: Round [104] log likelihood: -3733.758805
EM: Round [105] log likelihood: -3733.758040
EM: Round [106] log likelihood: -3733.757311
EM: Round [107] log likelihood: -3733.756617
EM: Round [108] log likelihood: -3733.755955
EM: Round [109] log likelihood: -3733.755324
EM: Round [110] log likelihood: -3733.754723
EM: Round [111] log likelihood: -3733.754150
EM: Round [112] log likelihood: -3733.753603
EM: Round [113] log likelihood: -3733.753083
EM: Round [114] log likelihood: -3733.752587
EM: Round [115] log likelihood: -3733.752115
EM: Round [116] log likelihood: -3733.751665
EM: Round [117] log likelihood: -3733.751236
EM: Round [118] log likelihood: -3733.750828
EM: Round [119] log likelihood: -3733.750439
EM: Round [120] log likelihood: -3733.750068
EM: Round [121] log likelihood: -3733.749715
EM: Round [122] log likelihood: -3733.749379
EM: Round [123] log likelihood: -3733.749059
EM: Round [124] log likelihood: -3733.748754
EM: Round [125] log likelihood: -3733.748464
EM: Round [126] log likelihood: -3733.748187
EM: Round [127] log likelihood: -3733.747924
EM: Round [128] log likelihood: -3733.747673
EM: Round [129] log likelihood: -3733.747435
EM: Round [130] log likelihood: -3733.747207
EM: Round [131] log likelihood: -3733.746991
EM: Round [132] log likelihood: -3733.746785
EM: Round [133] log likelihood: -3733.746589
EM: Round [134] log likelihood: -3733.746402
EM: Round [135] log likelihood: -3733.746224
EM: Round [136] log likelihood: -3733.746055
EM: Round [137] log likelihood: -3733.745894
EM: Round [138] log likelihood: -3733.745741
EM: Round [139] log likelihood: -3733.745595
EM: Round [140] log likelihood: -3733.745456
EM: Round [141] log likelihood: -3733.745324
EM: Round [142] log likelihood: -3733.745198
EM: Round [143] log likelihood: -3733.745079
EM: Round [144] log likelihood: -3733.744965
EM: Round [145] log likelihood: -3733.744856
EM: Round [146] log likelihood: -3733.744753
EM: Round [147] log likelihood: -3733.744655
EM: Stopping iterations at round 147 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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295222772
Execution Time = 5.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.OFF5IVX0JR/fi_workdir/microH.dat
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.OFF5IVX0JR/fi_workdir/microH.dat /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/fi_workdir/microH.dat /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.OFF5IVX0JR --json_outfile /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bGc-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.OFF5IVX0JR --json_outfile /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bGc-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.OFF5IVX0JR/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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bGc-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bGc-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir > /tmp/nxf.OFF5IVX0JR/659_bGc-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.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000241549.8]
WARNING, no entry stored in dbm for [ENSG00000241549.8]
WARNING, no entry stored in dbm for [ENSG00000282508.2]
WARNING, no entry stored in dbm for [ENSG00000224533.4]
WARNING, no entry stored in dbm for [ENSG00000224533.4]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.OFF5IVX0JR/ctat_genome_lib_build_dir > /tmp/nxf.OFF5IVX0JR/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.OFF5IVX0JR/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory