Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/07ceeaac91efe0f36bd706b1dc276f/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
  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/77/e0d4fca38a8cbb7592bbf3a31f4d8e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e0d4fca38a8cbb7592bbf3a31f4d8e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/b69d105f2c4c3bbd740585d6987707/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/b69d105f2c4c3bbd740585d6987707/659_rd-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_rd-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.tExeCh6s5b/659_rd-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_rd-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.tExeCh6s5b/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.tExeCh6s5b/cytoBand.txt
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.tExeCh6s5b/fi_workdir --reads "/tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:28:52 ..... started STAR run
Jun 08 09:28:52 ..... loading genome
Jun 08 09:30:36 ... generating Suffix Array index
Jun 08 09:34:22 ... completed Suffix Array index
Jun 08 09:34:22 ..... processing annotations GTF
Jun 08 09:34:22 ..... inserting junctions into the genome indices
Jun 08 09:35:23 ..... started mapping
Jun 08 10:28:49 ..... finished mapping
Jun 08 10:28:51 ..... started sorting BAM
Jun 08 10:28:53 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_rd-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_rd-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 60.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.tExeCh6s5b/fi_workdir --reads "/tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
10:29:13 : INFO : Done.
Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[3130000]   -done parsing /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 8538,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4774,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
          'exons hit < 2' => 9,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 13,
          ' ** passed ** ' => 86732,
          'low complexity anchor region' => 164,
          'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 48,
          'excessive soft clipping' => 14574,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 14,
          'small anchor length' => 1032,
          'num genes matched < 2' => 675,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 439,
          'seq-similar region overlap' => 1950
        };
-writing fusion junction support info.
Execution Time = 1.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[50000]   -fusion SPANNING read extraction for scaff: AL591378.1--DMD
-fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

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[1092000]   
[1093000]   
[1094000]   
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[1096000]   
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[1098000]   
[1099000]   
[1100000]   
[1101000]   
[1102000]   
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[1108000]   
[1109000]   
[1110000]   
[1111000]   
[1112000]   
[1113000]   
[1114000]   
[1115000]   
[1116000]   
[1117000]   
[1118000]   
[1119000]   -fusion SPANNING read extraction for scaff: NAB2--STAT6

[1000]   
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[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[20000]   
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[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[20000]   
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[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   -fusion SPANNING read extraction for scaff: PCDHA7--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[13000]   
[14000]   
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[16000]   
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[19000]   
[20000]   
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[24000]   
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[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[20000]   
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[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
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[15000]   
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[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[20000]   
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[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
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[20000]   
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[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
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[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[18000]   
[19000]   
[20000]   
[21000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[1109000]   -fusion SPANNING read extraction for scaff: STAT6--NAB2

[1000]   
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[55000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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

[1000]   
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[33000]   -fusion SPANNING read extraction for scaff: TMEM14B--FER1L5

[1000]   
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[14000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
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[49000]   -fusion SPANNING read extraction for scaff: XACT--LRRTM4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 40031,
          'lacks exon overlap' => 83379
        };
Execution Time = 5.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -28022.081655
EM: Round [1] log likelihood: -27862.529170
EM: Round [2] log likelihood: -27842.984221
EM: Round [3] log likelihood: -27829.961751
EM: Round [4] log likelihood: -27820.699505
EM: Round [5] log likelihood: -27814.022304
EM: Round [6] log likelihood: -27809.140933
EM: Round [7] log likelihood: -27805.515813
EM: Round [8] log likelihood: -27802.774392
EM: Round [9] log likelihood: -27800.657620
EM: Round [10] log likelihood: -27798.984458
EM: Round [11] log likelihood: -27797.627941
EM: Round [12] log likelihood: -27796.498800
EM: Round [13] log likelihood: -27795.534148
EM: Round [14] log likelihood: -27794.689605
EM: Round [15] log likelihood: -27793.933803
EM: Round [16] log likelihood: -27793.244525
EM: Round [17] log likelihood: -27792.605998
EM: Round [18] log likelihood: -27792.006989
EM: Round [19] log likelihood: -27791.439463
EM: Round [20] log likelihood: -27790.897641
EM: Round [21] log likelihood: -27790.377340
EM: Round [22] log likelihood: -27789.875498
EM: Round [23] log likelihood: -27789.389852
EM: Round [24] log likelihood: -27788.918703
EM: Round [25] log likelihood: -27788.460752
EM: Round [26] log likelihood: -27788.014989
EM: Round [27] log likelihood: -27787.580607
EM: Round [28] log likelihood: -27787.156950
EM: Round [29] log likelihood: -27786.743467
EM: Round [30] log likelihood: -27786.339687
EM: Round [31] log likelihood: -27785.945199
EM: Round [32] log likelihood: -27785.559636
EM: Round [33] log likelihood: -27785.182666
EM: Round [34] log likelihood: -27784.813981
EM: Round [35] log likelihood: -27784.453300
EM: Round [36] log likelihood: -27784.100354
EM: Round [37] log likelihood: -27783.754892
EM: Round [38] log likelihood: -27783.416677
EM: Round [39] log likelihood: -27783.085480
EM: Round [40] log likelihood: -27782.761084
EM: Round [41] log likelihood: -27782.443282
EM: Round [42] log likelihood: -27782.131874
EM: Round [43] log likelihood: -27781.826668
EM: Round [44] log likelihood: -27781.527480
EM: Round [45] log likelihood: -27781.234131
EM: Round [46] log likelihood: -27780.946453
EM: Round [47] log likelihood: -27780.664279
EM: Round [48] log likelihood: -27780.387451
EM: Round [49] log likelihood: -27780.115816
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EM: Round [967] log likelihood: -27757.221178
EM: Round [968] log likelihood: -27757.220903
EM: Round [969] log likelihood: -27757.220629
EM: Round [970] log likelihood: -27757.220356
EM: Round [971] log likelihood: -27757.220086
EM: Round [972] log likelihood: -27757.219817
EM: Round [973] log likelihood: -27757.219549
EM: Round [974] log likelihood: -27757.219284
EM: Round [975] log likelihood: -27757.219020
EM: Round [976] log likelihood: -27757.218757
EM: Round [977] log likelihood: -27757.218496
EM: Round [978] log likelihood: -27757.218237
EM: Round [979] log likelihood: -27757.217979
EM: Round [980] log likelihood: -27757.217723
EM: Round [981] log likelihood: -27757.217468
EM: Round [982] log likelihood: -27757.217215
EM: Round [983] log likelihood: -27757.216963
EM: Round [984] log likelihood: -27757.216713
EM: Round [985] log likelihood: -27757.216465
EM: Round [986] log likelihood: -27757.216218
EM: Round [987] log likelihood: -27757.215972
EM: Round [988] log likelihood: -27757.215728
EM: Round [989] log likelihood: -27757.215485
EM: Round [990] log likelihood: -27757.215244
EM: Round [991] log likelihood: -27757.215005
EM: Round [992] log likelihood: -27757.214766
EM: Round [993] log likelihood: -27757.214530
EM: Round [994] log likelihood: -27757.214294
EM: Round [995] log likelihood: -27757.214061
EM: Round [996] log likelihood: -27757.213828
EM: Round [997] log likelihood: -27757.213597
EM: Round [998] log likelihood: -27757.213367
EM: Round [999] log likelihood: -27757.213139
EM: Round [1000] log likelihood: -27757.212912
EM: Round [1001] log likelihood: -27757.212687
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/659_rd-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/fi_workdir/659_rd-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.tExeCh6s5b/fi_workdir/659_rd-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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir
-done, see /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -24629.476793
EM: Round [1] log likelihood: -24531.877036
EM: Round [2] log likelihood: -24530.785641
EM: Round [3] log likelihood: -24530.780129
EM: Round [4] log likelihood: -24530.780106
EM: Stopping iterations at round 4 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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 209192447
Execution Time = 4.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.tExeCh6s5b/fi_workdir/microH.dat
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.tExeCh6s5b/fi_workdir/microH.dat /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/fi_workdir/microH.dat /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.tExeCh6s5b --json_outfile /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_rd-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.tExeCh6s5b --json_outfile /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_rd-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.tExeCh6s5b/ctat_genome_lib_build_dir > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.tExeCh6s5b/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory