Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/8d865b731a0a558c15c7de1399d80b/aih-tih-sc-0419d4-R1_A23WJ53LT4_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/2f/152eb6a271af17680e0555f48a7480/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/82eb691afb36c58fdcf535755261e6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/82eb691afb36c58fdcf535755261e6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/8d865b731a0a558c15c7de1399d80b/aih-tih-sc-0419d4-R1_A23WJ53LT4_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 aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.ZgoIkpRV0X/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.ZgoIkpRV0X/cytoBand.txt
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed
-parsing GTF file: /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.ZgoIkpRV0X/fi_workdir --reads "/tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:24:42 ..... started STAR run
Jun 08 09:24:42 ..... loading genome
Jun 08 09:26:26 ... generating Suffix Array index
Jun 08 09:30:31 ... completed Suffix Array index
Jun 08 09:30:31 ..... processing annotations GTF
Jun 08 09:30:32 ..... inserting junctions into the genome indices
Jun 08 09:31:35 ..... started mapping
Jun 08 10:14:51 ..... finished mapping
Jun 08 10:14:53 ..... started sorting BAM
Jun 08 10:14:54 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
Execution Time = 50.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.ZgoIkpRV0X/fi_workdir --reads "/tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
10:15:04 : INFO : Done.
Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam

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[1890000]   -done parsing /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 6,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'num genes matched < 2' => 3,
          'excessive soft clipping' => 14533,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 28,
          ' ** passed ** ' => 11220,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
          'per_id < 96' => 10891,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 176,
          'seq-similar region overlap' => 381,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 17,
          'small anchor length' => 19,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3
        };
-writing fusion junction support info.
Execution Time = 1.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[15000]   -fusion SPANNING read extraction for scaff: AC004943.2--WWOX

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[3000]   -fusion SPANNING read extraction for scaff: AL669831.1--SEPTIN14

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[118000]   
[119000]   -fusion SPANNING read extraction for scaff: ATP13A4--OPA1

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[107000]   -fusion SPANNING read extraction for scaff: CREBBP--LINC02861

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[6000]   
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[8000]   
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[11000]   
[12000]   -fusion SPANNING read extraction for scaff: DDX19B--AC009060.2

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[179000]   
[180000]   -fusion SPANNING read extraction for scaff: FKBP5--SRPK1

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[89000]   
[90000]   
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[94000]   
[95000]   -fusion SPANNING read extraction for scaff: HIVEP3--ESRRG

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[8000]   
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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: INO80--NUSAP1

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[8000]   
[9000]   
[10000]   
[11000]   
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[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: LGALS8--EDARADD

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[360000]   
[361000]   -fusion SPANNING read extraction for scaff: MYH9--TXN2

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[8000]   
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[57000]   
[58000]   -fusion SPANNING read extraction for scaff: PCCA--CLYBL

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[6000]   
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[8000]   
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[27000]   
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[32000]   
[33000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[4000]   
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[8000]   
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[32000]   
[33000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[6000]   
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[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[9000]   
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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

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[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

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[27000]   
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[29000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

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[36000]   
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[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

[1000]   
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[13000]   
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[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

[1000]   
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[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
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[25000]   
[26000]   
[27000]   
[28000]   
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[31000]   
[32000]   
[33000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

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[28000]   
[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[16000]   
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[18000]   
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[20000]   
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[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

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[50000]   
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[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   -fusion SPANNING read extraction for scaff: PNPLA7--ZMYND19

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[40000]   
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[95000]   
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[100000]   
[101000]   
[102000]   
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[110000]   
[111000]   
[112000]   
[113000]   
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[120000]   
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[126000]   
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[129000]   
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[143000]   
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[148000]   
[149000]   
[150000]   
[151000]   
[152000]   
[153000]   
[154000]   
[155000]   
[156000]   -fusion SPANNING read extraction for scaff: PNPLA7--ARRDC1

[1000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[13000]   
[14000]   
[15000]   
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[26000]   
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[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: RNF111--MINDY2

[1000]   
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[6000]   
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[18000]   
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[20000]   
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[24000]   
[25000]   
[26000]   -fusion SPANNING read extraction for scaff: RNF169--POLD3

[1000]   
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[6000]   
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[8000]   
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[33000]   
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[39000]   
[40000]   
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[48000]   
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[50000]   
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[61000]   
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[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   -fusion SPANNING read extraction for scaff: TBC1D22A--GRAMD4

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[6000]   
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[8000]   
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[25000]   
[26000]   
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[30000]   
[31000]   
[32000]   
[33000]   -fusion SPANNING read extraction for scaff: WAPL--AL731569.1

[1000]   
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[8000]   
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[33000]   -fusion SPANNING read extraction for scaff: WAPL--RPL7AP8
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 6879,
          'seq similar region alignment' => 65001
        };
Execution Time = 2.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -3005.335728
EM: Round [1] log likelihood: -3000.279441
EM: Round [2] log likelihood: -2998.132781
EM: Round [3] log likelihood: -2997.010723
EM: Round [4] log likelihood: -2996.296180
EM: Round [5] log likelihood: -2995.762482
EM: Round [6] log likelihood: -2995.321486
EM: Round [7] log likelihood: -2994.937051
EM: Round [8] log likelihood: -2994.593123
EM: Round [9] log likelihood: -2994.281623
EM: Round [10] log likelihood: -2993.997761
EM: Round [11] log likelihood: -2993.738214
EM: Round [12] log likelihood: -2993.500392
EM: Round [13] log likelihood: -2993.282132
EM: Round [14] log likelihood: -2993.081564
EM: Round [15] log likelihood: -2992.897037
EM: Round [16] log likelihood: -2992.727086
EM: Round [17] log likelihood: -2992.570396
EM: Round [18] log likelihood: -2992.425789
EM: Round [19] log likelihood: -2992.292201
EM: Round [20] log likelihood: -2992.168675
EM: Round [21] log likelihood: -2992.054344
EM: Round [22] log likelihood: -2991.948423
EM: Round [23] log likelihood: -2991.850200
EM: Round [24] log likelihood: -2991.759029
EM: Round [25] log likelihood: -2991.674322
EM: Round [26] log likelihood: -2991.595545
EM: Round [27] log likelihood: -2991.522210
EM: Round [28] log likelihood: -2991.453872
EM: Round [29] log likelihood: -2991.390126
EM: Round [30] log likelihood: -2991.330602
EM: Round [31] log likelihood: -2991.274960
EM: Round [32] log likelihood: -2991.222891
EM: Round [33] log likelihood: -2991.174112
EM: Round [34] log likelihood: -2991.128363
EM: Round [35] log likelihood: -2991.085405
EM: Round [36] log likelihood: -2991.045022
EM: Round [37] log likelihood: -2991.007013
EM: Round [38] log likelihood: -2990.971194
EM: Round [39] log likelihood: -2990.937397
EM: Round [40] log likelihood: -2990.905468
EM: Round [41] log likelihood: -2990.875265
EM: Round [42] log likelihood: -2990.846657
EM: Round [43] log likelihood: -2990.819523
EM: Round [44] log likelihood: -2990.793755
EM: Round [45] log likelihood: -2990.769250
EM: Round [46] log likelihood: -2990.745916
EM: Round [47] log likelihood: -2990.723665
EM: Round [48] log likelihood: -2990.702420
EM: Round [49] log likelihood: -2990.682108
EM: Round [50] log likelihood: -2990.662661
EM: Round [51] log likelihood: -2990.644018
EM: Round [52] log likelihood: -2990.626121
EM: Round [53] log likelihood: -2990.608920
EM: Round [54] log likelihood: -2990.592364
EM: Round [55] log likelihood: -2990.576410
EM: Round [56] log likelihood: -2990.561016
EM: Round [57] log likelihood: -2990.546145
EM: Round [58] log likelihood: -2990.531761
EM: Round [59] log likelihood: -2990.517832
EM: Round [60] log likelihood: -2990.504329
EM: Round [61] log likelihood: -2990.491224
EM: Round [62] log likelihood: -2990.478491
EM: Round [63] log likelihood: -2990.466107
EM: Round [64] log likelihood: -2990.454049
EM: Round [65] log likelihood: -2990.442299
EM: Round [66] log likelihood: -2990.430837
EM: Round [67] log likelihood: -2990.419646
EM: Round [68] log likelihood: -2990.408711
EM: Round [69] log likelihood: -2990.398016
EM: Round [70] log likelihood: -2990.387547
EM: Round [71] log likelihood: -2990.377293
EM: Round [72] log likelihood: -2990.367241
EM: Round [73] log likelihood: -2990.357380
EM: Round [74] log likelihood: -2990.347701
EM: Round [75] log likelihood: -2990.338194
EM: Round [76] log likelihood: -2990.328851
EM: Round [77] log likelihood: -2990.319662
EM: Round [78] log likelihood: -2990.310621
EM: Round [79] log likelihood: -2990.301721
EM: Round [80] log likelihood: -2990.292956
EM: Round [81] log likelihood: -2990.284318
EM: Round [82] log likelihood: -2990.275803
EM: Round [83] log likelihood: -2990.267405
EM: Round [84] log likelihood: -2990.259120
EM: Round [85] log likelihood: -2990.250942
EM: Round [86] log likelihood: -2990.242868
EM: Round [87] log likelihood: -2990.234894
EM: Round [88] log likelihood: -2990.227016
EM: Round [89] log likelihood: -2990.219230
EM: Round [90] log likelihood: -2990.211533
EM: Round [91] log likelihood: -2990.203922
EM: Round [92] log likelihood: -2990.196394
EM: Round [93] log likelihood: -2990.188947
EM: Round [94] log likelihood: -2990.181578
EM: Round [95] log likelihood: -2990.174284
EM: Round [96] log likelihood: -2990.167064
EM: Round [97] log likelihood: -2990.159915
EM: Round [98] log likelihood: -2990.152835
EM: Round [99] log likelihood: -2990.145823
EM: Round [100] log likelihood: -2990.138876
EM: Round [101] log likelihood: -2990.131994
EM: Round [102] log likelihood: -2990.125173
EM: Round [103] log likelihood: -2990.118414
EM: Round [104] log likelihood: -2990.111714
EM: Round [105] log likelihood: -2990.105072
EM: Round [106] log likelihood: -2990.098487
EM: Round [107] log likelihood: -2990.091958
EM: Round [108] log likelihood: -2990.085483
EM: Round [109] log likelihood: -2990.079062
EM: Round [110] log likelihood: -2990.072692
EM: Round [111] log likelihood: -2990.066375
EM: Round [112] log likelihood: -2990.060107
EM: Round [113] log likelihood: -2990.053889
EM: Round [114] log likelihood: -2990.047720
EM: Round [115] log likelihood: -2990.041598
EM: Round [116] log likelihood: -2990.035523
EM: Round [117] log likelihood: -2990.029495
EM: Round [118] log likelihood: -2990.023512
EM: Round [119] log likelihood: -2990.017573
EM: Round [120] log likelihood: -2990.011679
EM: Round [121] log likelihood: -2990.005828
EM: Round [122] log likelihood: -2990.000019
EM: Round [123] log likelihood: -2989.994253
EM: Round [124] log likelihood: -2989.988528
EM: Round [125] log likelihood: -2989.982843
EM: Round [126] log likelihood: -2989.977200
EM: Round [127] log likelihood: -2989.971596
EM: Round [128] log likelihood: -2989.966031
EM: Round [129] log likelihood: -2989.960505
EM: Round [130] log likelihood: -2989.955017
EM: Round [131] log likelihood: -2989.949567
EM: Round [132] log likelihood: -2989.944154
EM: Round [133] log likelihood: -2989.938778
EM: Round [134] log likelihood: -2989.933439
EM: Round [135] log likelihood: -2989.928135
EM: Round [136] log likelihood: -2989.922867
EM: Round [137] log likelihood: -2989.917634
EM: Round [138] log likelihood: -2989.912436
EM: Round [139] log likelihood: -2989.907272
EM: Round [140] log likelihood: -2989.902142
EM: Round [141] log likelihood: -2989.897045
EM: Round [142] log likelihood: -2989.891982
EM: Round [143] log likelihood: -2989.886951
EM: Round [144] log likelihood: -2989.881953
EM: Round [145] log likelihood: -2989.876987
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EM: Round [610] log likelihood: -2988.972856
EM: Round [611] log likelihood: -2988.972173
EM: Round [612] log likelihood: -2988.971493
EM: Round [613] log likelihood: -2988.970816
EM: Round [614] log likelihood: -2988.970140
EM: Round [615] log likelihood: -2988.969467
EM: Round [616] log likelihood: -2988.968796
EM: Round [617] log likelihood: -2988.968127
EM: Round [618] log likelihood: -2988.967460
EM: Round [619] log likelihood: -2988.966796
EM: Round [620] log likelihood: -2988.966133
EM: Round [621] log likelihood: -2988.965473
EM: Round [622] log likelihood: -2988.964815
EM: Round [623] log likelihood: -2988.964159
EM: Round [624] log likelihood: -2988.963506
EM: Round [625] log likelihood: -2988.962854
EM: Round [626] log likelihood: -2988.962205
EM: Round [627] log likelihood: -2988.961558
EM: Round [628] log likelihood: -2988.960912
EM: Round [629] log likelihood: -2988.960269
EM: Round [630] log likelihood: -2988.959628
EM: Round [631] log likelihood: -2988.958990
EM: Round [632] log likelihood: -2988.958353
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EM: Round [634] log likelihood: -2988.957086
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EM: Round [637] log likelihood: -2988.955200
EM: Round [638] log likelihood: -2988.954576
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EM: Round [640] log likelihood: -2988.953333
EM: Round [641] log likelihood: -2988.952714
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EM: Round [643] log likelihood: -2988.951484
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EM: Round [652] log likelihood: -2988.946043
EM: Round [653] log likelihood: -2988.945448
EM: Round [654] log likelihood: -2988.944856
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EM: Round [656] log likelihood: -2988.943676
EM: Round [657] log likelihood: -2988.943088
EM: Round [658] log likelihood: -2988.942503
EM: Round [659] log likelihood: -2988.941920
EM: Round [660] log likelihood: -2988.941338
EM: Round [661] log likelihood: -2988.940759
EM: Round [662] log likelihood: -2988.940181
EM: Round [663] log likelihood: -2988.939605
EM: Round [664] log likelihood: -2988.939031
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EM: Round [666] log likelihood: -2988.937888
EM: Round [667] log likelihood: -2988.937319
EM: Round [668] log likelihood: -2988.936753
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EM: Round [670] log likelihood: -2988.935624
EM: Round [671] log likelihood: -2988.935063
EM: Round [672] log likelihood: -2988.934503
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EM: Round [674] log likelihood: -2988.933390
EM: Round [675] log likelihood: -2988.932835
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EM: Round [680] log likelihood: -2988.930090
EM: Round [681] log likelihood: -2988.929547
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EM: Round [685] log likelihood: -2988.927389
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EM: Round [713] log likelihood: -2988.913023
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EM: Round [721] log likelihood: -2988.909145
EM: Round [722] log likelihood: -2988.908667
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EM: Round [741] log likelihood: -2988.899861
EM: Round [742] log likelihood: -2988.899412
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EM: Round [744] log likelihood: -2988.898518
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EM: Round [746] log likelihood: -2988.897629
EM: Round [747] log likelihood: -2988.897186
EM: Round [748] log likelihood: -2988.896745
EM: Round [749] log likelihood: -2988.896306
EM: Round [750] log likelihood: -2988.895867
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EM: Round [765] log likelihood: -2988.889451
EM: Round [766] log likelihood: -2988.889033
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EM: Round [768] log likelihood: -2988.888202
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EM: Round [784] log likelihood: -2988.881733
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EM: Round [786] log likelihood: -2988.880946
EM: Round [787] log likelihood: -2988.880554
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EM: Round [789] log likelihood: -2988.879775
EM: Round [790] log likelihood: -2988.879386
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EM: Round [799] log likelihood: -2988.875946
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EM: Round [801] log likelihood: -2988.875194
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EM: Round [803] log likelihood: -2988.874446
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EM: Round [806] log likelihood: -2988.873333
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EM: Round [808] log likelihood: -2988.872597
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EM: Round [811] log likelihood: -2988.871500
EM: Round [812] log likelihood: -2988.871137
EM: Round [813] log likelihood: -2988.870775
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EM: Round [815] log likelihood: -2988.870054
EM: Round [816] log likelihood: -2988.869695
EM: Round [817] log likelihood: -2988.869337
EM: Round [818] log likelihood: -2988.868980
EM: Round [819] log likelihood: -2988.868624
EM: Round [820] log likelihood: -2988.868269
EM: Round [821] log likelihood: -2988.867916
EM: Round [822] log likelihood: -2988.867563
EM: Round [823] log likelihood: -2988.867212
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EM: Round [825] log likelihood: -2988.866512
EM: Round [826] log likelihood: -2988.866163
EM: Round [827] log likelihood: -2988.865816
EM: Round [828] log likelihood: -2988.865469
EM: Round [829] log likelihood: -2988.865124
EM: Round [830] log likelihood: -2988.864780
EM: Round [831] log likelihood: -2988.864436
EM: Round [832] log likelihood: -2988.864094
EM: Round [833] log likelihood: -2988.863753
EM: Round [834] log likelihood: -2988.863413
EM: Round [835] log likelihood: -2988.863073
EM: Round [836] log likelihood: -2988.862735
EM: Round [837] log likelihood: -2988.862398
EM: Round [838] log likelihood: -2988.862062
EM: Round [839] log likelihood: -2988.861726
EM: Round [840] log likelihood: -2988.861392
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EM: Round [842] log likelihood: -2988.860727
EM: Round [843] log likelihood: -2988.860395
EM: Round [844] log likelihood: -2988.860065
EM: Round [845] log likelihood: -2988.859736
EM: Round [846] log likelihood: -2988.859407
EM: Round [847] log likelihood: -2988.859080
EM: Round [848] log likelihood: -2988.858753
EM: Round [849] log likelihood: -2988.858428
EM: Round [850] log likelihood: -2988.858103
EM: Round [851] log likelihood: -2988.857780
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EM: Round [866] log likelihood: -2988.853038
EM: Round [867] log likelihood: -2988.852729
EM: Round [868] log likelihood: -2988.852422
EM: Round [869] log likelihood: -2988.852115
EM: Round [870] log likelihood: -2988.851809
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EM: Round [873] log likelihood: -2988.850896
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EM: Round [882] log likelihood: -2988.848205
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EM: Round [885] log likelihood: -2988.847324
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EM: Round [889] log likelihood: -2988.846160
EM: Round [890] log likelihood: -2988.845872
EM: Round [891] log likelihood: -2988.845584
EM: Round [892] log likelihood: -2988.845297
EM: Round [893] log likelihood: -2988.845010
EM: Round [894] log likelihood: -2988.844725
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EM: Round [896] log likelihood: -2988.844157
EM: Round [897] log likelihood: -2988.843874
EM: Round [898] log likelihood: -2988.843592
EM: Round [899] log likelihood: -2988.843311
EM: Round [900] log likelihood: -2988.843030
EM: Round [901] log likelihood: -2988.842750
EM: Round [902] log likelihood: -2988.842472
EM: Round [903] log likelihood: -2988.842193
EM: Round [904] log likelihood: -2988.841916
EM: Round [905] log likelihood: -2988.841640
EM: Round [906] log likelihood: -2988.841364
EM: Round [907] log likelihood: -2988.841089
EM: Round [908] log likelihood: -2988.840815
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EM: Round [910] log likelihood: -2988.840270
EM: Round [911] log likelihood: -2988.839998
EM: Round [912] log likelihood: -2988.839727
EM: Round [913] log likelihood: -2988.839457
EM: Round [914] log likelihood: -2988.839187
EM: Round [915] log likelihood: -2988.838919
EM: Round [916] log likelihood: -2988.838651
EM: Round [917] log likelihood: -2988.838384
EM: Round [918] log likelihood: -2988.838118
EM: Round [919] log likelihood: -2988.837852
EM: Round [920] log likelihood: -2988.837587
EM: Round [921] log likelihood: -2988.837323
EM: Round [922] log likelihood: -2988.837060
EM: Round [923] log likelihood: -2988.836798
EM: Round [924] log likelihood: -2988.836536
EM: Round [925] log likelihood: -2988.836275
EM: Round [926] log likelihood: -2988.836015
EM: Round [927] log likelihood: -2988.835755
EM: Round [928] log likelihood: -2988.835497
EM: Round [929] log likelihood: -2988.835239
EM: Round [930] log likelihood: -2988.834981
EM: Round [931] log likelihood: -2988.834725
EM: Round [932] log likelihood: -2988.834469
EM: Round [933] log likelihood: -2988.834214
EM: Round [934] log likelihood: -2988.833960
EM: Round [935] log likelihood: -2988.833706
EM: Round [936] log likelihood: -2988.833453
EM: Round [937] log likelihood: -2988.833201
EM: Round [938] log likelihood: -2988.832950
EM: Round [939] log likelihood: -2988.832699
EM: Round [940] log likelihood: -2988.832449
EM: Round [941] log likelihood: -2988.832200
EM: Round [942] log likelihood: -2988.831951
EM: Round [943] log likelihood: -2988.831703
EM: Round [944] log likelihood: -2988.831456
EM: Round [945] log likelihood: -2988.831210
EM: Round [946] log likelihood: -2988.830964
EM: Round [947] log likelihood: -2988.830719
EM: Round [948] log likelihood: -2988.830474
EM: Round [949] log likelihood: -2988.830231
EM: Round [950] log likelihood: -2988.829988
EM: Round [951] log likelihood: -2988.829745
EM: Round [952] log likelihood: -2988.829504
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EM: Round [954] log likelihood: -2988.829023
EM: Round [955] log likelihood: -2988.828783
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EM: Round [958] log likelihood: -2988.828069
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EM: Round [961] log likelihood: -2988.827360
EM: Round [962] log likelihood: -2988.827125
EM: Round [963] log likelihood: -2988.826891
EM: Round [964] log likelihood: -2988.826658
EM: Round [965] log likelihood: -2988.826425
EM: Round [966] log likelihood: -2988.826193
EM: Round [967] log likelihood: -2988.825961
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EM: Round [969] log likelihood: -2988.825500
EM: Round [970] log likelihood: -2988.825270
EM: Round [971] log likelihood: -2988.825042
EM: Round [972] log likelihood: -2988.824813
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EM: Round [974] log likelihood: -2988.824359
EM: Round [975] log likelihood: -2988.824132
EM: Round [976] log likelihood: -2988.823907
EM: Round [977] log likelihood: -2988.823682
EM: Round [978] log likelihood: -2988.823457
EM: Round [979] log likelihood: -2988.823233
EM: Round [980] log likelihood: -2988.823010
EM: Round [981] log likelihood: -2988.822788
EM: Round [982] log likelihood: -2988.822566
EM: Round [983] log likelihood: -2988.822345
EM: Round [984] log likelihood: -2988.822124
EM: Round [985] log likelihood: -2988.821904
EM: Round [986] log likelihood: -2988.821684
EM: Round [987] log likelihood: -2988.821466
EM: Round [988] log likelihood: -2988.821247
EM: Round [989] log likelihood: -2988.821030
EM: Round [990] log likelihood: -2988.820813
EM: Round [991] log likelihood: -2988.820597
EM: Round [992] log likelihood: -2988.820381
EM: Round [993] log likelihood: -2988.820166
EM: Round [994] log likelihood: -2988.819951
EM: Round [995] log likelihood: -2988.819737
EM: Round [996] log likelihood: -2988.819524
EM: Round [997] log likelihood: -2988.819311
EM: Round [998] log likelihood: -2988.819099
EM: Round [999] log likelihood: -2988.818887
EM: Round [1000] log likelihood: -2988.818676
EM: Round [1001] log likelihood: -2988.818466
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.48 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa > /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir
-done, see /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2634.415508
EM: Round [1] log likelihood: -2634.415508
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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 189923055
Execution Time = 3.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf  > /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf  > /tmp/nxf.ZgoIkpRV0X/fi_workdir/microH.dat
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.ZgoIkpRV0X/fi_workdir/microH.dat /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/fi_workdir/microH.dat /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.ZgoIkpRV0X --json_outfile /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-0419d4-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.ZgoIkpRV0X --json_outfile /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-0419d4-R1_A23WJ53LT4_1
Running: touch /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-0419d4-R1_A23WJ53LT4_1 --html_output /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-0419d4-R1_A23WJ53LT4_1 --html_output /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000262185.3]
WARNING, no entry stored in dbm for [ENSG00000262185.3]
WARNING, no entry stored in dbm for [ENSG00000261145.1]
WARNING, no entry stored in dbm for [ENSG00000259768.6]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.ZgoIkpRV0X/ctat_genome_lib_build_dir > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.ZgoIkpRV0X/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory