Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/d33575db21deb95009f2582dabc6c4/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/7778d871f750e93966b889bb7a6c96/.command.sh
  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/e6/7778d871f750e93966b889bb7a6c96/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/d33575db21deb95009f2582dabc6c4/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/83dc74367d9d8cfa5198999e18e9fe/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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 aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf > /tmp/nxf.9oQPqywk6G/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf > /tmp/nxf.9oQPqywk6G/cytoBand.txt
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed
-parsing GTF file: /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.9oQPqywk6G/fi_workdir --reads "/tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:26:08 ..... started STAR run
Jun 08 10:26:08 ..... loading genome
Jun 08 10:27:50 ... generating Suffix Array index
Jun 08 10:32:10 ... completed Suffix Array index
Jun 08 10:32:10 ..... processing annotations GTF
Jun 08 10:32:11 ..... inserting junctions into the genome indices
Jun 08 10:33:15 ..... started mapping
Jun 08 11:27:25 ..... finished mapping
Jun 08 11:27:26 ..... started sorting BAM
Jun 08 11:27:27 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
Execution Time = 61.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.9oQPqywk6G/fi_workdir --reads "/tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:27:35 : INFO : Done.
Execution Time = 0.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam

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[1340000]   -done parsing /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'seq-similar region overlap' => 47,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 69,
          'small anchor length' => 12,
          'excessive soft clipping' => 16607,
          ' ** passed ** ' => 6511,
          'exons hit < 2' => 5,
          'num genes matched < 2' => 77,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 35,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 8,
          'per_id < 96' => 8844,
          'low complexity anchor region' => 3
        };
-writing fusion junction support info.
Execution Time = 0.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[142000]   -fusion SPANNING read extraction for scaff: ACBD5--ARMC4P1

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[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   -fusion SPANNING read extraction for scaff: CREBBP--TRAP1

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[6000]   
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[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   -fusion SPANNING read extraction for scaff: ENG--ST6GALNAC6

[1000]   
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[6000]   
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[230000]   
[231000]   
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[233000]   
[234000]   
[235000]   
[236000]   -fusion SPANNING read extraction for scaff: ILF2--VPS72

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[11000]   
[12000]   
[13000]   
[14000]   
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[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: IMMP2L--DOCK4

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[91000]   
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[100000]   
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[111000]   
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[120000]   
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[130000]   
[131000]   
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[136000]   
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[139000]   
[140000]   
[141000]   
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[143000]   
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[145000]   
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[148000]   
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[150000]   
[151000]   
[152000]   
[153000]   
[154000]   
[155000]   
[156000]   -fusion SPANNING read extraction for scaff: LYST--NID1

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[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]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
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[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
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[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[11000]   
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[13000]   
[14000]   
[15000]   
[16000]   
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[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -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--PCDHGA9

[1000]   
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[4000]   
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[6000]   
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[100000]   
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[110000]   
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[120000]   
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[130000]   
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[133000]   
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[205000]   
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[209000]   
[210000]   
[211000]   -fusion SPANNING read extraction for scaff: PIP5K1A--ILF2

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[100000]   
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[110000]   
[111000]   
[112000]   -fusion SPANNING read extraction for scaff: RBM14--RBM4B

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[28000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 63435,
          'lacks exon overlap' => 5433
        };
Execution Time = 1.84 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2155.660237
EM: Round [1] log likelihood: -2154.159070
EM: Round [2] log likelihood: -2153.081628
EM: Round [3] log likelihood: -2152.267348
EM: Round [4] log likelihood: -2151.633224
EM: Round [5] log likelihood: -2151.129712
EM: Round [6] log likelihood: -2150.724571
EM: Round [7] log likelihood: -2150.395522
EM: Round [8] log likelihood: -2150.126452
EM: Round [9] log likelihood: -2149.905307
EM: Round [10] log likelihood: -2149.722829
EM: Round [11] log likelihood: -2149.571771
EM: Round [12] log likelihood: -2149.446379
EM: Round [13] log likelihood: -2149.342035
EM: Round [14] log likelihood: -2149.255006
EM: Round [15] log likelihood: -2149.182253
EM: Round [16] log likelihood: -2149.121295
EM: Round [17] log likelihood: -2149.070095
EM: Round [18] log likelihood: -2149.026980
EM: Round [19] log likelihood: -2148.990571
EM: Round [20] log likelihood: -2148.959729
EM: Round [21] log likelihood: -2148.933513
EM: Round [22] log likelihood: -2148.911144
EM: Round [23] log likelihood: -2148.891978
EM: Round [24] log likelihood: -2148.875478
EM: Round [25] log likelihood: -2148.861201
EM: Round [26] log likelihood: -2148.848780
EM: Round [27] log likelihood: -2148.837907
EM: Round [28] log likelihood: -2148.828330
EM: Round [29] log likelihood: -2148.819836
EM: Round [30] log likelihood: -2148.812250
EM: Round [31] log likelihood: -2148.805427
EM: Round [32] log likelihood: -2148.799244
EM: Round [33] log likelihood: -2148.793600
EM: Round [34] log likelihood: -2148.788411
EM: Round [35] log likelihood: -2148.783608
EM: Round [36] log likelihood: -2148.779131
EM: Round [37] log likelihood: -2148.774932
EM: Round [38] log likelihood: -2148.770970
EM: Round [39] log likelihood: -2148.767213
EM: Round [40] log likelihood: -2148.763630
EM: Round [41] log likelihood: -2148.760200
EM: Round [42] log likelihood: -2148.756901
EM: Round [43] log likelihood: -2148.753719
EM: Round [44] log likelihood: -2148.750637
EM: Round [45] log likelihood: -2148.747647
EM: Round [46] log likelihood: -2148.744736
EM: Round [47] log likelihood: -2148.741899
EM: Round [48] log likelihood: -2148.739126
EM: Round [49] log likelihood: -2148.736414
EM: Round [50] log likelihood: -2148.733756
EM: Round [51] log likelihood: -2148.731149
EM: Round [52] log likelihood: -2148.728589
EM: Round [53] log likelihood: -2148.726073
EM: Round [54] log likelihood: -2148.723599
EM: Round [55] log likelihood: -2148.721164
EM: Round [56] log likelihood: -2148.718767
EM: Round [57] log likelihood: -2148.716406
EM: Round [58] log likelihood: -2148.714078
EM: Round [59] log likelihood: -2148.711784
EM: Round [60] log likelihood: -2148.709522
EM: Round [61] log likelihood: -2148.707291
EM: Round [62] log likelihood: -2148.705090
EM: Round [63] log likelihood: -2148.702918
EM: Round [64] log likelihood: -2148.700775
EM: Round [65] log likelihood: -2148.698659
EM: Round [66] log likelihood: -2148.696571
EM: Round [67] log likelihood: -2148.694509
EM: Round [68] log likelihood: -2148.692474
EM: Round [69] log likelihood: -2148.690464
EM: Round [70] log likelihood: -2148.688480
EM: Round [71] log likelihood: -2148.686520
EM: Round [72] log likelihood: -2148.684584
EM: Round [73] log likelihood: -2148.682673
EM: Round [74] log likelihood: -2148.680785
EM: Round [75] log likelihood: -2148.678920
EM: Round [76] log likelihood: -2148.677078
EM: Round [77] log likelihood: -2148.675258
EM: Round [78] log likelihood: -2148.673461
EM: Round [79] log likelihood: -2148.671685
EM: Round [80] log likelihood: -2148.669931
EM: Round [81] log likelihood: -2148.668198
EM: Round [82] log likelihood: -2148.666486
EM: Round [83] log likelihood: -2148.664794
EM: Round [84] log likelihood: -2148.663123
EM: Round [85] log likelihood: -2148.661472
EM: Round [86] log likelihood: -2148.659840
EM: Round [87] log likelihood: -2148.658228
EM: Round [88] log likelihood: -2148.656635
EM: Round [89] log likelihood: -2148.655061
EM: Round [90] log likelihood: -2148.653506
EM: Round [91] log likelihood: -2148.651969
EM: Round [92] log likelihood: -2148.650450
EM: Round [93] log likelihood: -2148.648950
EM: Round [94] log likelihood: -2148.647467
EM: Round [95] log likelihood: -2148.646001
EM: Round [96] log likelihood: -2148.644553
EM: Round [97] log likelihood: -2148.643121
EM: Round [98] log likelihood: -2148.641707
EM: Round [99] log likelihood: -2148.640309
EM: Round [100] log likelihood: -2148.638927
EM: Round [101] log likelihood: -2148.637561
EM: Round [102] log likelihood: -2148.636212
EM: Round [103] log likelihood: -2148.634878
EM: Round [104] log likelihood: -2148.633559
EM: Round [105] log likelihood: -2148.632256
EM: Round [106] log likelihood: -2148.630968
EM: Round [107] log likelihood: -2148.629695
EM: Round [108] log likelihood: -2148.628436
EM: Round [109] log likelihood: -2148.627192
EM: Round [110] log likelihood: -2148.625963
EM: Round [111] log likelihood: -2148.624748
EM: Round [112] log likelihood: -2148.623546
EM: Round [113] log likelihood: -2148.622358
EM: Round [114] log likelihood: -2148.621185
EM: Round [115] log likelihood: -2148.620024
EM: Round [116] log likelihood: -2148.618877
EM: Round [117] log likelihood: -2148.617743
EM: Round [118] log likelihood: -2148.616622
EM: Round [119] log likelihood: -2148.615513
EM: Round [120] log likelihood: -2148.614417
EM: Round [121] log likelihood: -2148.613334
EM: Round [122] log likelihood: -2148.612263
EM: Round [123] log likelihood: -2148.611205
EM: Round [124] log likelihood: -2148.610158
EM: Round [125] log likelihood: -2148.609123
EM: Round [126] log likelihood: -2148.608100
EM: Round [127] log likelihood: -2148.607088
EM: Round [128] log likelihood: -2148.606088
EM: Round [129] log likelihood: -2148.605099
EM: Round [130] log likelihood: -2148.604122
EM: Round [131] log likelihood: -2148.603155
EM: Round [132] log likelihood: -2148.602199
EM: Round [133] log likelihood: -2148.601254
EM: Round [134] log likelihood: -2148.600320
EM: Round [135] log likelihood: -2148.599396
EM: Round [136] log likelihood: -2148.598482
EM: Round [137] log likelihood: -2148.597579
EM: Round [138] log likelihood: -2148.596686
EM: Round [139] log likelihood: -2148.595803
EM: Round [140] log likelihood: -2148.594929
EM: Round [141] log likelihood: -2148.594066
EM: Round [142] log likelihood: -2148.593212
EM: Round [143] log likelihood: -2148.592367
EM: Round [144] log likelihood: -2148.591532
EM: Round [145] log likelihood: -2148.590707
EM: Round [146] log likelihood: -2148.589890
EM: Round [147] log likelihood: -2148.589083
EM: Round [148] log likelihood: -2148.588284
EM: Round [149] log likelihood: -2148.587494
EM: Round [150] log likelihood: -2148.586714
EM: Round [151] log likelihood: -2148.585941
EM: Round [152] log likelihood: -2148.585178
EM: Round [153] log likelihood: -2148.584422
EM: Round [154] log likelihood: -2148.583676
EM: Round [155] log likelihood: -2148.582937
EM: Round [156] log likelihood: -2148.582206
EM: Round [157] log likelihood: -2148.581484
EM: Round [158] log likelihood: -2148.580770
EM: Round [159] log likelihood: -2148.580063
EM: Round [160] log likelihood: -2148.579364
EM: Round [161] log likelihood: -2148.578673
EM: Round [162] log likelihood: -2148.577989
EM: Round [163] log likelihood: -2148.577313
EM: Round [164] log likelihood: -2148.576645
EM: Round [165] log likelihood: -2148.575983
EM: Round [166] log likelihood: -2148.575329
EM: Round [167] log likelihood: -2148.574683
EM: Round [168] log likelihood: -2148.574043
EM: Round [169] log likelihood: -2148.573410
EM: Round [170] log likelihood: -2148.572784
EM: Round [171] log likelihood: -2148.572165
EM: Round [172] log likelihood: -2148.571553
EM: Round [173] log likelihood: -2148.570947
EM: Round [174] log likelihood: -2148.570348
EM: Round [175] log likelihood: -2148.569756
EM: Round [176] log likelihood: -2148.569170
EM: Round [177] log likelihood: -2148.568590
EM: Round [178] log likelihood: -2148.568017
EM: Round [179] log likelihood: -2148.567450
EM: Round [180] log likelihood: -2148.566889
EM: Round [181] log likelihood: -2148.566334
EM: Round [182] log likelihood: -2148.565785
EM: Round [183] log likelihood: -2148.565242
EM: Round [184] log likelihood: -2148.564705
EM: Round [185] log likelihood: -2148.564174
EM: Round [186] log likelihood: -2148.563649
EM: Round [187] log likelihood: -2148.563129
EM: Round [188] log likelihood: -2148.562615
EM: Round [189] log likelihood: -2148.562106
EM: Round [190] log likelihood: -2148.561603
EM: Round [191] log likelihood: -2148.561106
EM: Round [192] log likelihood: -2148.560613
EM: Round [193] log likelihood: -2148.560127
EM: Round [194] log likelihood: -2148.559645
EM: Round [195] log likelihood: -2148.559168
EM: Round [196] log likelihood: -2148.558697
EM: Round [197] log likelihood: -2148.558231
EM: Round [198] log likelihood: -2148.557770
EM: Round [199] log likelihood: -2148.557313
EM: Round [200] log likelihood: -2148.556862
EM: Round [201] log likelihood: -2148.556415
EM: Round [202] log likelihood: -2148.555974
EM: Round [203] log likelihood: -2148.555537
EM: Round [204] log likelihood: -2148.555105
EM: Round [205] log likelihood: -2148.554677
EM: Round [206] log likelihood: -2148.554254
EM: Round [207] log likelihood: -2148.553835
EM: Round [208] log likelihood: -2148.553421
EM: Round [209] log likelihood: -2148.553012
EM: Round [210] log likelihood: -2148.552607
EM: Round [211] log likelihood: -2148.552206
EM: Round [212] log likelihood: -2148.551809
EM: Round [213] log likelihood: -2148.551417
EM: Round [214] log likelihood: -2148.551029
EM: Round [215] log likelihood: -2148.550645
EM: Round [216] log likelihood: -2148.550265
EM: Round [217] log likelihood: -2148.549889
EM: Round [218] log likelihood: -2148.549517
EM: Round [219] log likelihood: -2148.549149
EM: Round [220] log likelihood: -2148.548786
EM: Round [221] log likelihood: -2148.548426
EM: Round [222] log likelihood: -2148.548069
EM: Round [223] log likelihood: -2148.547717
EM: Round [224] log likelihood: -2148.547368
EM: Round [225] log likelihood: -2148.547023
EM: Round [226] log likelihood: -2148.546682
EM: Round [227] log likelihood: -2148.546345
EM: Round [228] log likelihood: -2148.546011
EM: Round [229] log likelihood: -2148.545680
EM: Round [230] log likelihood: -2148.545353
EM: Round [231] log likelihood: -2148.545030
EM: Round [232] log likelihood: -2148.544710
EM: Round [233] log likelihood: -2148.544393
EM: Round [234] log likelihood: -2148.544080
EM: Round [235] log likelihood: -2148.543770
EM: Round [236] log likelihood: -2148.543463
EM: Round [237] log likelihood: -2148.543160
EM: Round [238] log likelihood: -2148.542859
EM: Round [239] log likelihood: -2148.542562
EM: Round [240] log likelihood: -2148.542269
EM: Round [241] log likelihood: -2148.541978
EM: Round [242] log likelihood: -2148.541690
EM: Round [243] log likelihood: -2148.541406
EM: Round [244] log likelihood: -2148.541124
EM: Round [245] log likelihood: -2148.540845
EM: Round [246] log likelihood: -2148.540570
EM: Round [247] log likelihood: -2148.540297
EM: Round [248] log likelihood: -2148.540027
EM: Round [249] log likelihood: -2148.539760
EM: Round [250] log likelihood: -2148.539496
EM: Round [251] log likelihood: -2148.539235
EM: Round [252] log likelihood: -2148.538976
EM: Round [253] log likelihood: -2148.538720
EM: Round [254] log likelihood: -2148.538467
EM: Round [255] log likelihood: -2148.538216
EM: Round [256] log likelihood: -2148.537968
EM: Round [257] log likelihood: -2148.537723
EM: Round [258] log likelihood: -2148.537480
EM: Round [259] log likelihood: -2148.537240
EM: Round [260] log likelihood: -2148.537003
EM: Round [261] log likelihood: -2148.536768
EM: Round [262] log likelihood: -2148.536535
EM: Round [263] log likelihood: -2148.536305
EM: Round [264] log likelihood: -2148.536077
EM: Round [265] log likelihood: -2148.535852
EM: Round [266] log likelihood: -2148.535629
EM: Round [267] log likelihood: -2148.535408
EM: Round [268] log likelihood: -2148.535190
EM: Round [269] log likelihood: -2148.534974
EM: Round [270] log likelihood: -2148.534760
EM: Round [271] log likelihood: -2148.534549
EM: Round [272] log likelihood: -2148.534340
EM: Round [273] log likelihood: -2148.534133
EM: Round [274] log likelihood: -2148.533928
EM: Round [275] log likelihood: -2148.533725
EM: Round [276] log likelihood: -2148.533524
EM: Round [277] log likelihood: -2148.533326
EM: Round [278] log likelihood: -2148.533130
EM: Round [279] log likelihood: -2148.532935
EM: Round [280] log likelihood: -2148.532743
EM: Round [281] log likelihood: -2148.532553
EM: Round [282] log likelihood: -2148.532364
EM: Round [283] log likelihood: -2148.532178
EM: Round [284] log likelihood: -2148.531994
EM: Round [285] log likelihood: -2148.531811
EM: Round [286] log likelihood: -2148.531631
EM: Round [287] log likelihood: -2148.531452
EM: Round [288] log likelihood: -2148.531275
EM: Round [289] log likelihood: -2148.531101
EM: Round [290] log likelihood: -2148.530928
EM: Round [291] log likelihood: -2148.530756
EM: Round [292] log likelihood: -2148.530587
EM: Round [293] log likelihood: -2148.530419
EM: Round [294] log likelihood: -2148.530253
EM: Round [295] log likelihood: -2148.530089
EM: Round [296] log likelihood: -2148.529927
EM: Round [297] log likelihood: -2148.529766
EM: Round [298] log likelihood: -2148.529607
EM: Round [299] log likelihood: -2148.529450
EM: Round [300] log likelihood: -2148.529294
EM: Round [301] log likelihood: -2148.529140
EM: Round [302] log likelihood: -2148.528987
EM: Round [303] log likelihood: -2148.528836
EM: Round [304] log likelihood: -2148.528687
EM: Round [305] log likelihood: -2148.528539
EM: Round [306] log likelihood: -2148.528393
EM: Round [307] log likelihood: -2148.528248
EM: Round [308] log likelihood: -2148.528105
EM: Round [309] log likelihood: -2148.527963
EM: Round [310] log likelihood: -2148.527823
EM: Round [311] log likelihood: -2148.527684
EM: Round [312] log likelihood: -2148.527547
EM: Round [313] log likelihood: -2148.527411
EM: Round [314] log likelihood: -2148.527277
EM: Round [315] log likelihood: -2148.527144
EM: Round [316] log likelihood: -2148.527012
EM: Round [317] log likelihood: -2148.526882
EM: Round [318] log likelihood: -2148.526753
EM: Round [319] log likelihood: -2148.526625
EM: Round [320] log likelihood: -2148.526499
EM: Round [321] log likelihood: -2148.526374
EM: Round [322] log likelihood: -2148.526250
EM: Round [323] log likelihood: -2148.526128
EM: Round [324] log likelihood: -2148.526007
EM: Round [325] log likelihood: -2148.525887
EM: Round [326] log likelihood: -2148.525769
EM: Round [327] log likelihood: -2148.525651
EM: Round [328] log likelihood: -2148.525535
EM: Round [329] log likelihood: -2148.525420
EM: Round [330] log likelihood: -2148.525307
EM: Round [331] log likelihood: -2148.525194
EM: Round [332] log likelihood: -2148.525083
EM: Round [333] log likelihood: -2148.524973
EM: Round [334] log likelihood: -2148.524864
EM: Round [335] log likelihood: -2148.524756
EM: Round [336] log likelihood: -2148.524649
EM: Round [337] log likelihood: -2148.524543
EM: Round [338] log likelihood: -2148.524439
EM: Round [339] log likelihood: -2148.524335
EM: Round [340] log likelihood: -2148.524233
EM: Round [341] log likelihood: -2148.524132
EM: Round [342] log likelihood: -2148.524032
EM: Round [343] log likelihood: -2148.523932
EM: Stopping iterations at round 343 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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa > /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir
-done, see /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2105.943858
EM: Round [1] log likelihood: -2105.943858
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 250381754
Execution Time = 4.84 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf  > /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.gtf  > /tmp/nxf.9oQPqywk6G/fi_workdir/microH.dat
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.9oQPqywk6G/fi_workdir/microH.dat /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/fi_workdir/microH.dat /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.9oQPqywk6G --json_outfile /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-1351d2-R1_A23WJ53LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.9oQPqywk6G --json_outfile /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-1351d2-R1_A23WJ53LT4_1
Running: touch /tmp/nxf.9oQPqywk6G/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.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-1351d2-R1_A23WJ53LT4_1 --html_output /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_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.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-1351d2-R1_A23WJ53LT4_1 --html_output /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000280136.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.9oQPqywk6G/ctat_genome_lib_build_dir > /tmp/nxf.9oQPqywk6G/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.9oQPqywk6G/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory