Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/f420a71141fefe510b53decda37cee/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz
  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/85/c4549ec15652dd3169157f63a4d7c5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/31e7917f8b02475297f66a193bffb4/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/c4549ec15652dd3169157f63a4d7c5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/f420a71141fefe510b53decda37cee/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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 1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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 1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.n7GLtfdPXZ/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.n7GLtfdPXZ/cytoBand.txt
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed
-parsing GTF file: /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.n7GLtfdPXZ/fi_workdir --reads "/tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 11:35:50 ..... started STAR run
Jun 08 11:35:50 ..... loading genome
Jun 08 11:37:30 ... generating Suffix Array index
Jun 08 11:41:16 ... completed Suffix Array index
Jun 08 11:41:17 ..... processing annotations GTF
Jun 08 11:41:17 ..... inserting junctions into the genome indices
Jun 08 11:42:17 ..... started mapping
Jun 08 12:23:52 ..... finished mapping
Jun 08 12:23:54 ..... started sorting BAM
Jun 08 12:23:54 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
Execution Time = 48.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.n7GLtfdPXZ/fi_workdir --reads "/tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
12:23:58 : INFO : Done.
Execution Time = 0.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam

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[730000]   -done parsing /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 82,
          'low complexity anchor region' => 30,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 40,
          'seq-similar region overlap' => 201,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 637,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 3,
          'small anchor length' => 160,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
          'exons hit < 2' => 6,
          'excessive soft clipping' => 4694,
          ' ** passed ** ' => 15364,
          'per_id < 96' => 2934,
          'num genes matched < 2' => 16
        };
-writing fusion junction support info.
Execution Time = 0.38 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[100000]   -fusion SPANNING read extraction for scaff: ADAM9--AC087354.1

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[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   -fusion SPANNING read extraction for scaff: PCDHB14--PCDHB15

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[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: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[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]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   
[119000]   
[120000]   
[121000]   
[122000]   
[123000]   
[124000]   
[125000]   
[126000]   
[127000]   
[128000]   
[129000]   
[130000]   
[131000]   
[132000]   
[133000]   
[134000]   
[135000]   
[136000]   
[137000]   
[138000]   
[139000]   
[140000]   
[141000]   
[142000]   
[143000]   
[144000]   
[145000]   
[146000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
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[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]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
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[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]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   -fusion SPANNING read extraction for scaff: USP22--SLC9A8
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 56126,
          'lacks exon overlap' => 3355
        };
Execution Time = 0.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2197.215673
EM: Round [1] log likelihood: -2197.061894
EM: Round [2] log likelihood: -2197.037425
EM: Round [3] log likelihood: -2197.016382
EM: Round [4] log likelihood: -2196.995689
EM: Round [5] log likelihood: -2196.975265
EM: Round [6] log likelihood: -2196.955103
EM: Round [7] log likelihood: -2196.935197
EM: Round [8] log likelihood: -2196.915540
EM: Round [9] log likelihood: -2196.896129
EM: Round [10] log likelihood: -2196.876956
EM: Round [11] log likelihood: -2196.858017
EM: Round [12] log likelihood: -2196.839307
EM: Round [13] log likelihood: -2196.820821
EM: Round [14] log likelihood: -2196.802555
EM: Round [15] log likelihood: -2196.784503
EM: Round [16] log likelihood: -2196.766661
EM: Round [17] log likelihood: -2196.749026
EM: Round [18] log likelihood: -2196.731593
EM: Round [19] log likelihood: -2196.714357
EM: Round [20] log likelihood: -2196.697315
EM: Round [21] log likelihood: -2196.680464
EM: Round [22] log likelihood: -2196.663799
EM: Round [23] log likelihood: -2196.647316
EM: Round [24] log likelihood: -2196.631013
EM: Round [25] log likelihood: -2196.614887
EM: Round [26] log likelihood: -2196.598933
EM: Round [27] log likelihood: -2196.583148
EM: Round [28] log likelihood: -2196.567530
EM: Round [29] log likelihood: -2196.552075
EM: Round [30] log likelihood: -2196.536780
EM: Round [31] log likelihood: -2196.521644
EM: Round [32] log likelihood: -2196.506662
EM: Round [33] log likelihood: -2196.491832
EM: Round [34] log likelihood: -2196.477151
EM: Round [35] log likelihood: -2196.462617
EM: Round [36] log likelihood: -2196.448228
EM: Round [37] log likelihood: -2196.433980
EM: Round [38] log likelihood: -2196.419872
EM: Round [39] log likelihood: -2196.405900
EM: Round [40] log likelihood: -2196.392064
EM: Round [41] log likelihood: -2196.378361
EM: Round [42] log likelihood: -2196.364787
EM: Round [43] log likelihood: -2196.351343
EM: Round [44] log likelihood: -2196.338024
EM: Round [45] log likelihood: -2196.324830
EM: Round [46] log likelihood: -2196.311758
EM: Round [47] log likelihood: -2196.298807
EM: Round [48] log likelihood: -2196.285974
EM: Round [49] log likelihood: -2196.273257
EM: Round [50] log likelihood: -2196.260656
EM: Round [51] log likelihood: -2196.248168
EM: Round [52] log likelihood: -2196.235791
EM: Round [53] log likelihood: -2196.223524
EM: Round [54] log likelihood: -2196.211365
EM: Round [55] log likelihood: -2196.199312
EM: Round [56] log likelihood: -2196.187365
EM: Round [57] log likelihood: -2196.175521
EM: Round [58] log likelihood: -2196.163779
EM: Round [59] log likelihood: -2196.152137
EM: Round [60] log likelihood: -2196.140595
EM: Round [61] log likelihood: -2196.129150
EM: Round [62] log likelihood: -2196.117801
EM: Round [63] log likelihood: -2196.106548
EM: Round [64] log likelihood: -2196.095387
EM: Round [65] log likelihood: -2196.084319
EM: Round [66] log likelihood: -2196.073343
EM: Round [67] log likelihood: -2196.062456
EM: Round [68] log likelihood: -2196.051657
EM: Round [69] log likelihood: -2196.040946
EM: Round [70] log likelihood: -2196.030321
EM: Round [71] log likelihood: -2196.019781
EM: Round [72] log likelihood: -2196.009325
EM: Round [73] log likelihood: -2195.998952
EM: Round [74] log likelihood: -2195.988661
EM: Round [75] log likelihood: -2195.978450
EM: Round [76] log likelihood: -2195.968319
EM: Round [77] log likelihood: -2195.958267
EM: Round [78] log likelihood: -2195.948292
EM: Round [79] log likelihood: -2195.938394
EM: Round [80] log likelihood: -2195.928572
EM: Round [81] log likelihood: -2195.918825
EM: Round [82] log likelihood: -2195.909151
EM: Round [83] log likelihood: -2195.899550
EM: Round [84] log likelihood: -2195.890021
EM: Round [85] log likelihood: -2195.880564
EM: Round [86] log likelihood: -2195.871176
EM: Round [87] log likelihood: -2195.861858
EM: Round [88] log likelihood: -2195.852609
EM: Round [89] log likelihood: -2195.843428
EM: Round [90] log likelihood: -2195.834313
EM: Round [91] log likelihood: -2195.825265
EM: Round [92] log likelihood: -2195.816282
EM: Round [93] log likelihood: -2195.807363
EM: Round [94] log likelihood: -2195.798509
EM: Round [95] log likelihood: -2195.789718
EM: Round [96] log likelihood: -2195.780989
EM: Round [97] log likelihood: -2195.772322
EM: Round [98] log likelihood: -2195.763716
EM: Round [99] log likelihood: -2195.755170
EM: Round [100] log likelihood: -2195.746684
EM: Round [101] log likelihood: -2195.738257
EM: Round [102] log likelihood: -2195.729888
EM: Round [103] log likelihood: -2195.721577
EM: Round [104] log likelihood: -2195.713323
EM: Round [105] log likelihood: -2195.705125
EM: Round [106] log likelihood: -2195.696983
EM: Round [107] log likelihood: -2195.688897
EM: Round [108] log likelihood: -2195.680865
EM: Round [109] log likelihood: -2195.672887
EM: Round [110] log likelihood: -2195.664962
EM: Round [111] log likelihood: -2195.657091
EM: Round [112] log likelihood: -2195.649271
EM: Round [113] log likelihood: -2195.641504
EM: Round [114] log likelihood: -2195.633788
EM: Round [115] log likelihood: -2195.626122
EM: Round [116] log likelihood: -2195.618507
EM: Round [117] log likelihood: -2195.610941
EM: Round [118] log likelihood: -2195.603424
EM: Round [119] log likelihood: -2195.595957
EM: Round [120] log likelihood: -2195.588537
EM: Round [121] log likelihood: -2195.581165
EM: Round [122] log likelihood: -2195.573840
EM: Round [123] log likelihood: -2195.566562
EM: Round [124] log likelihood: -2195.559330
EM: Round [125] log likelihood: -2195.552144
EM: Round [126] log likelihood: -2195.545003
EM: Round [127] log likelihood: -2195.537907
EM: Round [128] log likelihood: -2195.530855
EM: Round [129] log likelihood: -2195.523848
EM: Round [130] log likelihood: -2195.516884
EM: Round [131] log likelihood: -2195.509963
EM: Round [132] log likelihood: -2195.503085
EM: Round [133] log likelihood: -2195.496250
EM: Round [134] log likelihood: -2195.489456
EM: Round [135] log likelihood: -2195.482704
EM: Round [136] log likelihood: -2195.475993
EM: Round [137] log likelihood: -2195.469323
EM: Round [138] log likelihood: -2195.462693
EM: Round [139] log likelihood: -2195.456103
EM: Round [140] log likelihood: -2195.449553
EM: Round [141] log likelihood: -2195.443042
EM: Round [142] log likelihood: -2195.436570
EM: Round [143] log likelihood: -2195.430137
EM: Round [144] log likelihood: -2195.423742
EM: Round [145] log likelihood: -2195.417384
EM: Round [146] log likelihood: -2195.411064
EM: Round [147] log likelihood: -2195.404781
EM: Round [148] log likelihood: -2195.398536
EM: Round [149] log likelihood: -2195.392326
EM: Round [150] log likelihood: -2195.386153
EM: Round [151] log likelihood: -2195.380016
EM: Round [152] log likelihood: -2195.373914
EM: Round [153] log likelihood: -2195.367847
EM: Round [154] log likelihood: -2195.361815
EM: Round [155] log likelihood: -2195.355818
EM: Round [156] log likelihood: -2195.349855
EM: Round [157] log likelihood: -2195.343927
EM: Round [158] log likelihood: -2195.338032
EM: Round [159] log likelihood: -2195.332170
EM: Round [160] log likelihood: -2195.326341
EM: Round [161] log likelihood: -2195.320546
EM: Round [162] log likelihood: -2195.314783
EM: Round [163] log likelihood: -2195.309052
EM: Round [164] log likelihood: -2195.303353
EM: Round [165] log likelihood: -2195.297686
EM: Round [166] log likelihood: -2195.292051
EM: Round [167] log likelihood: -2195.286446
EM: Round [168] log likelihood: -2195.280873
EM: Round [169] log likelihood: -2195.275331
EM: Round [170] log likelihood: -2195.269819
EM: Round [171] log likelihood: -2195.264337
EM: Round [172] log likelihood: -2195.258885
EM: Round [173] log likelihood: -2195.253462
EM: Round [174] log likelihood: -2195.248070
EM: Round [175] log likelihood: -2195.242706
EM: Round [176] log likelihood: -2195.237372
EM: Round [177] log likelihood: -2195.232066
EM: Round [178] log likelihood: -2195.226789
EM: Round [179] log likelihood: -2195.221540
EM: Round [180] log likelihood: -2195.216319
EM: Round [181] log likelihood: -2195.211126
EM: Round [182] log likelihood: -2195.205961
EM: Round [183] log likelihood: -2195.200823
EM: Round [184] log likelihood: -2195.195712
EM: Round [185] log likelihood: -2195.190629
EM: Round [186] log likelihood: -2195.185572
EM: Round [187] log likelihood: -2195.180541
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EM: Round [997] log likelihood: -2193.988963
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EM: Round [999] log likelihood: -2193.988367
EM: Round [1000] log likelihood: -2193.988071
EM: Round [1001] log likelihood: -2193.987775
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir
-done, see /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1947.831156
EM: Round [1] log likelihood: -1947.661678
EM: Round [2] log likelihood: -1947.622002
EM: Round [3] log likelihood: -1947.586221
EM: Round [4] log likelihood: -1947.551238
EM: Round [5] log likelihood: -1947.516951
EM: Round [6] log likelihood: -1947.483334
EM: Round [7] log likelihood: -1947.450362
EM: Round [8] log likelihood: -1947.418014
EM: Round [9] log likelihood: -1947.386267
EM: Round [10] log likelihood: -1947.355101
EM: Round [11] log likelihood: -1947.324497
EM: Round [12] log likelihood: -1947.294437
EM: Round [13] log likelihood: -1947.264902
EM: Round [14] log likelihood: -1947.235876
EM: Round [15] log likelihood: -1947.207344
EM: Round [16] log likelihood: -1947.179289
EM: Round [17] log likelihood: -1947.151698
EM: Round [18] log likelihood: -1947.124556
EM: Round [19] log likelihood: -1947.097851
EM: Round [20] log likelihood: -1947.071570
EM: Round [21] log likelihood: -1947.045700
EM: Round [22] log likelihood: -1947.020230
EM: Round [23] log likelihood: -1946.995149
EM: Round [24] log likelihood: -1946.970446
EM: Round [25] log likelihood: -1946.946111
EM: Round [26] log likelihood: -1946.922135
EM: Round [27] log likelihood: -1946.898506
EM: Round [28] log likelihood: -1946.875218
EM: Round [29] log likelihood: -1946.852260
EM: Round [30] log likelihood: -1946.829625
EM: Round [31] log likelihood: -1946.807304
EM: Round [32] log likelihood: -1946.785290
EM: Round [33] log likelihood: -1946.763575
EM: Round [34] log likelihood: -1946.742151
EM: Round [35] log likelihood: -1946.721013
EM: Round [36] log likelihood: -1946.700153
EM: Round [37] log likelihood: -1946.679564
EM: Round [38] log likelihood: -1946.659241
EM: Round [39] log likelihood: -1946.639177
EM: Round [40] log likelihood: -1946.619367
EM: Round [41] log likelihood: -1946.599804
EM: Round [42] log likelihood: -1946.580484
EM: Round [43] log likelihood: -1946.561401
EM: Round [44] log likelihood: -1946.542550
EM: Round [45] log likelihood: -1946.523926
EM: Round [46] log likelihood: -1946.505525
EM: Round [47] log likelihood: -1946.487341
EM: Round [48] log likelihood: -1946.469369
EM: Round [49] log likelihood: -1946.451607
EM: Round [50] log likelihood: -1946.434049
EM: Round [51] log likelihood: -1946.416691
EM: Round [52] log likelihood: -1946.399530
EM: Round [53] log likelihood: -1946.382561
EM: Round [54] log likelihood: -1946.365781
EM: Round [55] log likelihood: -1946.349186
EM: Round [56] log likelihood: -1946.332773
EM: Round [57] log likelihood: -1946.316538
EM: Round [58] log likelihood: -1946.300477
EM: Round [59] log likelihood: -1946.284588
EM: Round [60] log likelihood: -1946.268867
EM: Round [61] log likelihood: -1946.253311
EM: Round [62] log likelihood: -1946.237918
EM: Round [63] log likelihood: -1946.222684
EM: Round [64] log likelihood: -1946.207607
EM: Round [65] log likelihood: -1946.192683
EM: Round [66] log likelihood: -1946.177910
EM: Round [67] log likelihood: -1946.163286
EM: Round [68] log likelihood: -1946.148807
EM: Round [69] log likelihood: -1946.134472
EM: Round [70] log likelihood: -1946.120278
EM: Round [71] log likelihood: -1946.106222
EM: Round [72] log likelihood: -1946.092303
EM: Round [73] log likelihood: -1946.078517
EM: Round [74] log likelihood: -1946.064863
EM: Round [75] log likelihood: -1946.051339
EM: Round [76] log likelihood: -1946.037943
EM: Round [77] log likelihood: -1946.024672
EM: Round [78] log likelihood: -1946.011525
EM: Round [79] log likelihood: -1945.998499
EM: Round [80] log likelihood: -1945.985593
EM: Round [81] log likelihood: -1945.972805
EM: Round [82] log likelihood: -1945.960132
EM: Round [83] log likelihood: -1945.947574
EM: Round [84] log likelihood: -1945.935129
EM: Round [85] log likelihood: -1945.922794
EM: Round [86] log likelihood: -1945.910568
EM: Round [87] log likelihood: -1945.898450
EM: Round [88] log likelihood: -1945.886438
EM: Round [89] log likelihood: -1945.874530
EM: Round [90] log likelihood: -1945.862725
EM: Round [91] log likelihood: -1945.851022
EM: Round [92] log likelihood: -1945.839418
EM: Round [93] log likelihood: -1945.827913
EM: Round [94] log likelihood: -1945.816505
EM: Round [95] log likelihood: -1945.805192
EM: Round [96] log likelihood: -1945.793975
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EM: Round [98] log likelihood: -1945.771817
EM: Round [99] log likelihood: -1945.760874
EM: Round [100] log likelihood: -1945.750021
EM: Round [101] log likelihood: -1945.739256
EM: Round [102] log likelihood: -1945.728578
EM: Round [103] log likelihood: -1945.717986
EM: Round [104] log likelihood: -1945.707478
EM: Round [105] log likelihood: -1945.697054
EM: Round [106] log likelihood: -1945.686712
EM: Round [107] log likelihood: -1945.676451
EM: Round [108] log likelihood: -1945.666271
EM: Round [109] log likelihood: -1945.656170
EM: Round [110] log likelihood: -1945.646148
EM: Round [111] log likelihood: -1945.636203
EM: Round [112] log likelihood: -1945.626334
EM: Round [113] log likelihood: -1945.616540
EM: Round [114] log likelihood: -1945.606821
EM: Round [115] log likelihood: -1945.597175
EM: Round [116] log likelihood: -1945.587602
EM: Round [117] log likelihood: -1945.578100
EM: Round [118] log likelihood: -1945.568669
EM: Round [119] log likelihood: -1945.559308
EM: Round [120] log likelihood: -1945.550017
EM: Round [121] log likelihood: -1945.540793
EM: Round [122] log likelihood: -1945.531637
EM: Round [123] log likelihood: -1945.522548
EM: Round [124] log likelihood: -1945.513525
EM: Round [125] log likelihood: -1945.504567
EM: Round [126] log likelihood: -1945.495673
EM: Round [127] log likelihood: -1945.486842
EM: Round [128] log likelihood: -1945.478075
EM: Round [129] log likelihood: -1945.469370
EM: Round [130] log likelihood: -1945.460726
EM: Round [131] log likelihood: -1945.452143
EM: Round [132] log likelihood: -1945.443620
EM: Round [133] log likelihood: -1945.435157
EM: Round [134] log likelihood: -1945.426752
EM: Round [135] log likelihood: -1945.418405
EM: Round [136] log likelihood: -1945.410116
EM: Round [137] log likelihood: -1945.401883
EM: Round [138] log likelihood: -1945.393707
EM: Round [139] log likelihood: -1945.385586
EM: Round [140] log likelihood: -1945.377521
EM: Round [141] log likelihood: -1945.369509
EM: Round [142] log likelihood: -1945.361552
EM: Round [143] log likelihood: -1945.353648
EM: Round [144] log likelihood: -1945.345796
EM: Round [145] log likelihood: -1945.337997
EM: Round [146] log likelihood: -1945.330249
EM: Round [147] log likelihood: -1945.322552
EM: Round [148] log likelihood: -1945.314905
EM: Round [149] log likelihood: -1945.307309
EM: Round [150] log likelihood: -1945.299762
EM: Round [151] log likelihood: -1945.292264
EM: Round [152] log likelihood: -1945.284815
EM: Round [153] log likelihood: -1945.277413
EM: Round [154] log likelihood: -1945.270059
EM: Round [155] log likelihood: -1945.262752
EM: Round [156] log likelihood: -1945.255492
EM: Round [157] log likelihood: -1945.248277
EM: Round [158] log likelihood: -1945.241108
EM: Round [159] log likelihood: -1945.233985
EM: Round [160] log likelihood: -1945.226906
EM: Round [161] log likelihood: -1945.219871
EM: Round [162] log likelihood: -1945.212880
EM: Round [163] log likelihood: -1945.205933
EM: Round [164] log likelihood: -1945.199029
EM: Round [165] log likelihood: -1945.192167
EM: Round [166] log likelihood: -1945.185347
EM: Round [167] log likelihood: -1945.178570
EM: Round [168] log likelihood: -1945.171833
EM: Round [169] log likelihood: -1945.165138
EM: Round [170] log likelihood: -1945.158483
EM: Round [171] log likelihood: -1945.151869
EM: Round [172] log likelihood: -1945.145294
EM: Round [173] log likelihood: -1945.138759
EM: Round [174] log likelihood: -1945.132263
EM: Round [175] log likelihood: -1945.125806
EM: Round [176] log likelihood: -1945.119387
EM: Round [177] log likelihood: -1945.113006
EM: Round [178] log likelihood: -1945.106663
EM: Round [179] log likelihood: -1945.100357
EM: Round [180] log likelihood: -1945.094088
EM: Round [181] log likelihood: -1945.087856
EM: Round [182] log likelihood: -1945.081661
EM: Round [183] log likelihood: -1945.075501
EM: Round [184] log likelihood: -1945.069378
EM: Round [185] log likelihood: -1945.063289
EM: Round [186] log likelihood: -1945.057236
EM: Round [187] log likelihood: -1945.051217
EM: Round [188] log likelihood: -1945.045233
EM: Round [189] log likelihood: -1945.039284
EM: Round [190] log likelihood: -1945.033368
EM: Round [191] log likelihood: -1945.027485
EM: Round [192] log likelihood: -1945.021636
EM: Round [193] log likelihood: -1945.015820
EM: Round [194] log likelihood: -1945.010037
EM: Round [195] log likelihood: -1945.004287
EM: Round [196] log likelihood: -1944.998568
EM: Round [197] log likelihood: -1944.992881
EM: Round [198] log likelihood: -1944.987226
EM: Round [199] log likelihood: -1944.981603
EM: Round [200] log likelihood: -1944.976011
EM: Round [201] log likelihood: -1944.970449
EM: Round [202] log likelihood: -1944.964918
EM: Round [203] log likelihood: -1944.959417
EM: Round [204] log likelihood: -1944.953947
EM: Round [205] log likelihood: -1944.948506
EM: Round [206] log likelihood: -1944.943095
EM: Round [207] log likelihood: -1944.937714
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EM: Round [209] log likelihood: -1944.927038
EM: Round [210] log likelihood: -1944.921743
EM: Round [211] log likelihood: -1944.916477
EM: Round [212] log likelihood: -1944.911239
EM: Round [213] log likelihood: -1944.906028
EM: Round [214] log likelihood: -1944.900846
EM: Round [215] log likelihood: -1944.895691
EM: Round [216] log likelihood: -1944.890564
EM: Round [217] log likelihood: -1944.885463
EM: Round [218] log likelihood: -1944.880390
EM: Round [219] log likelihood: -1944.875343
EM: Round [220] log likelihood: -1944.870323
EM: Round [221] log likelihood: -1944.865329
EM: Round [222] log likelihood: -1944.860361
EM: Round [223] log likelihood: -1944.855419
EM: Round [224] log likelihood: -1944.850503
EM: Round [225] log likelihood: -1944.845612
EM: Round [226] log likelihood: -1944.840747
EM: Round [227] log likelihood: -1944.835906
EM: Round [228] log likelihood: -1944.831091
EM: Round [229] log likelihood: -1944.826300
EM: Round [230] log likelihood: -1944.821534
EM: Round [231] log likelihood: -1944.816792
EM: Round [232] log likelihood: -1944.812074
EM: Round [233] log likelihood: -1944.807381
EM: Round [234] log likelihood: -1944.802711
EM: Round [235] log likelihood: -1944.798065
EM: Round [236] log likelihood: -1944.793442
EM: Round [237] log likelihood: -1944.788842
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EM: Round [240] log likelihood: -1944.775182
EM: Round [241] log likelihood: -1944.770674
EM: Round [242] log likelihood: -1944.766189
EM: Round [243] log likelihood: -1944.761726
EM: Round [244] log likelihood: -1944.757285
EM: Round [245] log likelihood: -1944.752866
EM: Round [246] log likelihood: -1944.748468
EM: Round [247] log likelihood: -1944.744093
EM: Round [248] log likelihood: -1944.739739
EM: Round [249] log likelihood: -1944.735406
EM: Round [250] log likelihood: -1944.731095
EM: Round [251] log likelihood: -1944.726804
EM: Round [252] log likelihood: -1944.722535
EM: Round [253] log likelihood: -1944.718286
EM: Round [254] log likelihood: -1944.714058
EM: Round [255] log likelihood: -1944.709851
EM: Round [256] log likelihood: -1944.705663
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EM: Round [258] log likelihood: -1944.697349
EM: Round [259] log likelihood: -1944.693222
EM: Round [260] log likelihood: -1944.689115
EM: Round [261] log likelihood: -1944.685028
EM: Round [262] log likelihood: -1944.680959
EM: Round [263] log likelihood: -1944.676911
EM: Round [264] log likelihood: -1944.672881
EM: Round [265] log likelihood: -1944.668871
EM: Round [266] log likelihood: -1944.664880
EM: Round [267] log likelihood: -1944.660907
EM: Round [268] log likelihood: -1944.656953
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EM: Round [271] log likelihood: -1944.645203
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EM: Round [278] log likelihood: -1944.618420
EM: Round [279] log likelihood: -1944.614664
EM: Round [280] log likelihood: -1944.610926
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EM: Round [312] log likelihood: -1944.499817
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EM: Round [955] log likelihood: -1943.705549
EM: Round [956] log likelihood: -1943.705179
EM: Round [957] log likelihood: -1943.704809
EM: Round [958] log likelihood: -1943.704440
EM: Round [959] log likelihood: -1943.704073
EM: Round [960] log likelihood: -1943.703707
EM: Round [961] log likelihood: -1943.703341
EM: Round [962] log likelihood: -1943.702977
EM: Round [963] log likelihood: -1943.702614
EM: Round [964] log likelihood: -1943.702252
EM: Round [965] log likelihood: -1943.701890
EM: Round [966] log likelihood: -1943.701530
EM: Round [967] log likelihood: -1943.701171
EM: Round [968] log likelihood: -1943.700813
EM: Round [969] log likelihood: -1943.700457
EM: Round [970] log likelihood: -1943.700101
EM: Round [971] log likelihood: -1943.699746
EM: Round [972] log likelihood: -1943.699392
EM: Round [973] log likelihood: -1943.699039
EM: Round [974] log likelihood: -1943.698688
EM: Round [975] log likelihood: -1943.698337
EM: Round [976] log likelihood: -1943.697987
EM: Round [977] log likelihood: -1943.697639
EM: Round [978] log likelihood: -1943.697291
EM: Round [979] log likelihood: -1943.696944
EM: Round [980] log likelihood: -1943.696599
EM: Round [981] log likelihood: -1943.696254
EM: Round [982] log likelihood: -1943.695911
EM: Round [983] log likelihood: -1943.695568
EM: Round [984] log likelihood: -1943.695226
EM: Round [985] log likelihood: -1943.694886
EM: Round [986] log likelihood: -1943.694546
EM: Round [987] log likelihood: -1943.694208
EM: Round [988] log likelihood: -1943.693870
EM: Round [989] log likelihood: -1943.693533
EM: Round [990] log likelihood: -1943.693198
EM: Round [991] log likelihood: -1943.692863
EM: Round [992] log likelihood: -1943.692529
EM: Round [993] log likelihood: -1943.692197
EM: Round [994] log likelihood: -1943.691865
EM: Round [995] log likelihood: -1943.691534
EM: Round [996] log likelihood: -1943.691204
EM: Round [997] log likelihood: -1943.690875
EM: Round [998] log likelihood: -1943.690547
EM: Round [999] log likelihood: -1943.690220
EM: Round [1000] log likelihood: -1943.689894
EM: Round [1001] log likelihood: -1943.689569
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 294836827
Execution Time = 5.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf  > /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.gtf  > /tmp/nxf.n7GLtfdPXZ/fi_workdir/microH.dat
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.n7GLtfdPXZ/fi_workdir/microH.dat /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/fi_workdir/microH.dat /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.n7GLtfdPXZ --json_outfile /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.n7GLtfdPXZ --json_outfile /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1
Running: touch /tmp/nxf.n7GLtfdPXZ/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.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_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.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.n7GLtfdPXZ/ctat_genome_lib_build_dir > /tmp/nxf.n7GLtfdPXZ/1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.n7GLtfdPXZ/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory