Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/7fe16015bc07a1545fab10918307a9/aih-tih-sc-b675f7-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/c1/1a5b1a676768ee5753ca5d817d499d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/1a5b1a676768ee5753ca5d817d499d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/d88aa1c8141ce2e4fb535ecc7faa79/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/7fe16015bc07a1545fab10918307a9/aih-tih-sc-b675f7-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-b675f7-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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-b675f7-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf > /tmp/nxf.juLjv4mr3C/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf > /tmp/nxf.juLjv4mr3C/cytoBand.txt
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed
-parsing GTF file: /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.juLjv4mr3C/fi_workdir --reads "/tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:36:12 ..... started STAR run
Jun 08 10:36:12 ..... loading genome
Jun 08 10:37:52 ... generating Suffix Array index
Jun 08 10:41:36 ... completed Suffix Array index
Jun 08 10:41:36 ..... processing annotations GTF
Jun 08 10:41:36 ..... inserting junctions into the genome indices
Jun 08 10:42:36 ..... started mapping
Jun 08 11:38:38 ..... finished mapping
Jun 08 11:38:39 ..... started sorting BAM
Jun 08 11:38:39 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
Execution Time = 62.47 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.juLjv4mr3C/fi_workdir --reads "/tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:38:44 : INFO : Done.
Execution Time = 0.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam

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[660000]   -done parsing /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 39,
          'small anchor length' => 23,
          'per_id < 96' => 1996,
          'exons hit < 2' => 2,
          ' ** passed ** ' => 10648,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 38,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9,
          'num genes matched < 2' => 13,
          'low complexity anchor region' => 21,
          'excessive soft clipping' => 2877,
          'seq-similar region overlap' => 217
        };
-writing fusion junction support info.
Execution Time = 0.32 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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-fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

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[80000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3

[1000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

[1000]   
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[3000]   
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[5000]   
[6000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

[1000]   
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[7000]   
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[12000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
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[3000]   
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[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

[1000]   
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[19000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

[1000]   
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[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[79000]   
[80000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

[1000]   
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[6000]   
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[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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

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

[1000]   
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[6000]   
[7000]   
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[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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

[1000]   
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[5000]   
[6000]   
[7000]   
[8000]   
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[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
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[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
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[6000]   
[7000]   
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[9000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
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[5000]   
[6000]   
[7000]   
[8000]   
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[10000]   
[11000]   
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[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
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[72000]   
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[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
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[6000]   
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[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157B

[1000]   
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[4000]   
[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
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[33000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 1389,
          'seq similar region alignment' => 30087
        };
Execution Time = 0.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -3949.407373
EM: Round [1] log likelihood: -3947.173782
EM: Round [2] log likelihood: -3946.074682
EM: Round [3] log likelihood: -3945.262496
EM: Round [4] log likelihood: -3944.650014
EM: Round [5] log likelihood: -3944.180262
EM: Round [6] log likelihood: -3943.814636
EM: Round [7] log likelihood: -3943.526262
EM: Round [8] log likelihood: -3943.295996
EM: Round [9] log likelihood: -3943.109935
EM: Round [10] log likelihood: -3942.957826
EM: Round [11] log likelihood: -3942.832012
EM: Round [12] log likelihood: -3942.726718
EM: Round [13] log likelihood: -3942.637557
EM: Round [14] log likelihood: -3942.561170
EM: Round [15] log likelihood: -3942.494973
EM: Round [16] log likelihood: -3942.436964
EM: Round [17] log likelihood: -3942.385585
EM: Round [18] log likelihood: -3942.339620
EM: Round [19] log likelihood: -3942.298108
EM: Round [20] log likelihood: -3942.260289
EM: Round [21] log likelihood: -3942.225561
EM: Round [22] log likelihood: -3942.193436
EM: Round [23] log likelihood: -3942.163524
EM: Round [24] log likelihood: -3942.135507
EM: Round [25] log likelihood: -3942.109126
EM: Round [26] log likelihood: -3942.084165
EM: Round [27] log likelihood: -3942.060448
EM: Round [28] log likelihood: -3942.037827
EM: Round [29] log likelihood: -3942.016177
EM: Round [30] log likelihood: -3941.995395
EM: Round [31] log likelihood: -3941.975391
EM: Round [32] log likelihood: -3941.956089
EM: Round [33] log likelihood: -3941.937425
EM: Round [34] log likelihood: -3941.919342
EM: Round [35] log likelihood: -3941.901791
EM: Round [36] log likelihood: -3941.884731
EM: Round [37] log likelihood: -3941.868125
EM: Round [38] log likelihood: -3941.851940
EM: Round [39] log likelihood: -3941.836147
EM: Round [40] log likelihood: -3941.820722
EM: Round [41] log likelihood: -3941.805642
EM: Round [42] log likelihood: -3941.790887
EM: Round [43] log likelihood: -3941.776439
EM: Round [44] log likelihood: -3941.762283
EM: Round [45] log likelihood: -3941.748403
EM: Round [46] log likelihood: -3941.734786
EM: Round [47] log likelihood: -3941.721421
EM: Round [48] log likelihood: -3941.708297
EM: Round [49] log likelihood: -3941.695404
EM: Round [50] log likelihood: -3941.682733
EM: Round [51] log likelihood: -3941.670275
EM: Round [52] log likelihood: -3941.658023
EM: Round [53] log likelihood: -3941.645970
EM: Round [54] log likelihood: -3941.634108
EM: Round [55] log likelihood: -3941.622432
EM: Round [56] log likelihood: -3941.610936
EM: Round [57] log likelihood: -3941.599614
EM: Round [58] log likelihood: -3941.588461
EM: Round [59] log likelihood: -3941.577473
EM: Round [60] log likelihood: -3941.566644
EM: Round [61] log likelihood: -3941.555971
EM: Round [62] log likelihood: -3941.545449
EM: Round [63] log likelihood: -3941.535075
EM: Round [64] log likelihood: -3941.524844
EM: Round [65] log likelihood: -3941.514753
EM: Round [66] log likelihood: -3941.504799
EM: Round [67] log likelihood: -3941.494979
EM: Round [68] log likelihood: -3941.485289
EM: Round [69] log likelihood: -3941.475726
EM: Round [70] log likelihood: -3941.466288
EM: Round [71] log likelihood: -3941.456971
EM: Round [72] log likelihood: -3941.447774
EM: Round [73] log likelihood: -3941.438692
EM: Round [74] log likelihood: -3941.429725
EM: Round [75] log likelihood: -3941.420870
EM: Round [76] log likelihood: -3941.412124
EM: Round [77] log likelihood: -3941.403485
EM: Round [78] log likelihood: -3941.394951
EM: Round [79] log likelihood: -3941.386519
EM: Round [80] log likelihood: -3941.378189
EM: Round [81] log likelihood: -3941.369957
EM: Round [82] log likelihood: -3941.361822
EM: Round [83] log likelihood: -3941.353782
EM: Round [84] log likelihood: -3941.345836
EM: Round [85] log likelihood: -3941.337981
EM: Round [86] log likelihood: -3941.330215
EM: Round [87] log likelihood: -3941.322538
EM: Round [88] log likelihood: -3941.314948
EM: Round [89] log likelihood: -3941.307443
EM: Round [90] log likelihood: -3941.300021
EM: Round [91] log likelihood: -3941.292681
EM: Round [92] log likelihood: -3941.285422
EM: Round [93] log likelihood: -3941.278242
EM: Round [94] log likelihood: -3941.271140
EM: Round [95] log likelihood: -3941.264115
EM: Round [96] log likelihood: -3941.257164
EM: Round [97] log likelihood: -3941.250288
EM: Round [98] log likelihood: -3941.243484
EM: Round [99] log likelihood: -3941.236752
EM: Round [100] log likelihood: -3941.230091
EM: Round [101] log likelihood: -3941.223499
EM: Round [102] log likelihood: -3941.216974
EM: Round [103] log likelihood: -3941.210517
EM: Round [104] log likelihood: -3941.204126
EM: Round [105] log likelihood: -3941.197800
EM: Round [106] log likelihood: -3941.191538
EM: Round [107] log likelihood: -3941.185338
EM: Round [108] log likelihood: -3941.179201
EM: Round [109] log likelihood: -3941.173125
EM: Round [110] log likelihood: -3941.167109
EM: Round [111] log likelihood: -3941.161152
EM: Round [112] log likelihood: -3941.155253
EM: Round [113] log likelihood: -3941.149412
EM: Round [114] log likelihood: -3941.143628
EM: Round [115] log likelihood: -3941.137899
EM: Round [116] log likelihood: -3941.132225
EM: Round [117] log likelihood: -3941.126606
EM: Round [118] log likelihood: -3941.121040
EM: Round [119] log likelihood: -3941.115526
EM: Round [120] log likelihood: -3941.110065
EM: Round [121] log likelihood: -3941.104655
EM: Round [122] log likelihood: -3941.099295
EM: Round [123] log likelihood: -3941.093985
EM: Round [124] log likelihood: -3941.088724
EM: Round [125] log likelihood: -3941.083512
EM: Round [126] log likelihood: -3941.078347
EM: Round [127] log likelihood: -3941.073230
EM: Round [128] log likelihood: -3941.068159
EM: Round [129] log likelihood: -3941.063133
EM: Round [130] log likelihood: -3941.058154
EM: Round [131] log likelihood: -3941.053218
EM: Round [132] log likelihood: -3941.048327
EM: Round [133] log likelihood: -3941.043480
EM: Round [134] log likelihood: -3941.038675
EM: Round [135] log likelihood: -3941.033913
EM: Round [136] log likelihood: -3941.029193
EM: Round [137] log likelihood: -3941.024514
EM: Round [138] log likelihood: -3941.019876
EM: Round [139] log likelihood: -3941.015278
EM: Round [140] log likelihood: -3941.010720
EM: Round [141] log likelihood: -3941.006201
EM: Round [142] log likelihood: -3941.001721
EM: Round [143] log likelihood: -3940.997279
EM: Round [144] log likelihood: -3940.992876
EM: Round [145] log likelihood: -3940.988509
EM: Round [146] log likelihood: -3940.984180
EM: Round [147] log likelihood: -3940.979887
EM: Round [148] log likelihood: -3940.975630
EM: Round [149] log likelihood: -3940.971409
EM: Round [150] log likelihood: -3940.967223
EM: Round [151] log likelihood: -3940.963072
EM: Round [152] log likelihood: -3940.958955
EM: Round [153] log likelihood: -3940.954873
EM: Round [154] log likelihood: -3940.950824
EM: Round [155] log likelihood: -3940.946808
EM: Round [156] log likelihood: -3940.942825
EM: Round [157] log likelihood: -3940.938874
EM: Round [158] log likelihood: -3940.934956
EM: Round [159] log likelihood: -3940.931069
EM: Round [160] log likelihood: -3940.927214
EM: Round [161] log likelihood: -3940.923389
EM: Round [162] log likelihood: -3940.919596
EM: Round [163] log likelihood: -3940.915833
EM: Round [164] log likelihood: -3940.912099
EM: Round [165] log likelihood: -3940.908396
EM: Round [166] log likelihood: -3940.904722
EM: Round [167] log likelihood: -3940.901076
EM: Round [168] log likelihood: -3940.897460
EM: Round [169] log likelihood: -3940.893872
EM: Round [170] log likelihood: -3940.890312
EM: Round [171] log likelihood: -3940.886780
EM: Round [172] log likelihood: -3940.883275
EM: Round [173] log likelihood: -3940.879798
EM: Round [174] log likelihood: -3940.876347
EM: Round [175] log likelihood: -3940.872923
EM: Round [176] log likelihood: -3940.869526
EM: Round [177] log likelihood: -3940.866154
EM: Round [178] log likelihood: -3940.862809
EM: Round [179] log likelihood: -3940.859489
EM: Round [180] log likelihood: -3940.856194
EM: Round [181] log likelihood: -3940.852924
EM: Round [182] log likelihood: -3940.849679
EM: Round [183] log likelihood: -3940.846459
EM: Round [184] log likelihood: -3940.843263
EM: Round [185] log likelihood: -3940.840091
EM: Round [186] log likelihood: -3940.836942
EM: Round [187] log likelihood: -3940.833817
EM: Round [188] log likelihood: -3940.830716
EM: Round [189] log likelihood: -3940.827638
EM: Round [190] log likelihood: -3940.824582
EM: Round [191] log likelihood: -3940.821549
EM: Round [192] log likelihood: -3940.818539
EM: Round [193] log likelihood: -3940.815551
EM: Round [194] log likelihood: -3940.812584
EM: Round [195] log likelihood: -3940.809640
EM: Round [196] log likelihood: -3940.806717
EM: Round [197] log likelihood: -3940.803815
EM: Round [198] log likelihood: -3940.800935
EM: Round [199] log likelihood: -3940.798075
EM: Round [200] log likelihood: -3940.795236
EM: Round [201] log likelihood: -3940.792418
EM: Round [202] log likelihood: -3940.789620
EM: Round [203] log likelihood: -3940.786842
EM: Round [204] log likelihood: -3940.784085
EM: Round [205] log likelihood: -3940.781346
EM: Round [206] log likelihood: -3940.778628
EM: Round [207] log likelihood: -3940.775929
EM: Round [208] log likelihood: -3940.773249
EM: Round [209] log likelihood: -3940.770589
EM: Round [210] log likelihood: -3940.767947
EM: Round [211] log likelihood: -3940.765324
EM: Round [212] log likelihood: -3940.762719
EM: Round [213] log likelihood: -3940.760133
EM: Round [214] log likelihood: -3940.757565
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EM: Round [675] log likelihood: -3940.367441
EM: Round [676] log likelihood: -3940.367260
EM: Round [677] log likelihood: -3940.367081
EM: Round [678] log likelihood: -3940.366902
EM: Round [679] log likelihood: -3940.366725
EM: Round [680] log likelihood: -3940.366548
EM: Round [681] log likelihood: -3940.366372
EM: Round [682] log likelihood: -3940.366197
EM: Round [683] log likelihood: -3940.366024
EM: Round [684] log likelihood: -3940.365851
EM: Round [685] log likelihood: -3940.365678
EM: Round [686] log likelihood: -3940.365507
EM: Round [687] log likelihood: -3940.365337
EM: Round [688] log likelihood: -3940.365168
EM: Round [689] log likelihood: -3940.364999
EM: Round [690] log likelihood: -3940.364831
EM: Round [691] log likelihood: -3940.364665
EM: Round [692] log likelihood: -3940.364499
EM: Round [693] log likelihood: -3940.364334
EM: Round [694] log likelihood: -3940.364169
EM: Round [695] log likelihood: -3940.364006
EM: Round [696] log likelihood: -3940.363844
EM: Round [697] log likelihood: -3940.363682
EM: Round [698] log likelihood: -3940.363521
EM: Round [699] log likelihood: -3940.363361
EM: Round [700] log likelihood: -3940.363202
EM: Round [701] log likelihood: -3940.363044
EM: Round [702] log likelihood: -3940.362887
EM: Round [703] log likelihood: -3940.362730
EM: Round [704] log likelihood: -3940.362574
EM: Round [705] log likelihood: -3940.362419
EM: Round [706] log likelihood: -3940.362265
EM: Round [707] log likelihood: -3940.362112
EM: Round [708] log likelihood: -3940.361959
EM: Round [709] log likelihood: -3940.361807
EM: Round [710] log likelihood: -3940.361656
EM: Round [711] log likelihood: -3940.361506
EM: Round [712] log likelihood: -3940.361357
EM: Round [713] log likelihood: -3940.361208
EM: Round [714] log likelihood: -3940.361060
EM: Round [715] log likelihood: -3940.360913
EM: Round [716] log likelihood: -3940.360767
EM: Round [717] log likelihood: -3940.360621
EM: Round [718] log likelihood: -3940.360477
EM: Round [719] log likelihood: -3940.360333
EM: Round [720] log likelihood: -3940.360189
EM: Round [721] log likelihood: -3940.360047
EM: Round [722] log likelihood: -3940.359905
EM: Round [723] log likelihood: -3940.359764
EM: Round [724] log likelihood: -3940.359624
EM: Round [725] log likelihood: -3940.359484
EM: Round [726] log likelihood: -3940.359345
EM: Round [727] log likelihood: -3940.359207
EM: Round [728] log likelihood: -3940.359069
EM: Round [729] log likelihood: -3940.358933
EM: Round [730] log likelihood: -3940.358797
EM: Round [731] log likelihood: -3940.358662
EM: Round [732] log likelihood: -3940.358527
EM: Round [733] log likelihood: -3940.358393
EM: Round [734] log likelihood: -3940.358260
EM: Round [735] log likelihood: -3940.358127
EM: Round [736] log likelihood: -3940.357996
EM: Round [737] log likelihood: -3940.357864
EM: Round [738] log likelihood: -3940.357734
EM: Round [739] log likelihood: -3940.357604
EM: Round [740] log likelihood: -3940.357475
EM: Round [741] log likelihood: -3940.357347
EM: Round [742] log likelihood: -3940.357219
EM: Round [743] log likelihood: -3940.357092
EM: Round [744] log likelihood: -3940.356966
EM: Round [745] log likelihood: -3940.356840
EM: Round [746] log likelihood: -3940.356715
EM: Round [747] log likelihood: -3940.356590
EM: Round [748] log likelihood: -3940.356466
EM: Round [749] log likelihood: -3940.356343
EM: Round [750] log likelihood: -3940.356221
EM: Round [751] log likelihood: -3940.356099
EM: Round [752] log likelihood: -3940.355978
EM: Round [753] log likelihood: -3940.355857
EM: Round [754] log likelihood: -3940.355737
EM: Round [755] log likelihood: -3940.355618
EM: Round [756] log likelihood: -3940.355499
EM: Round [757] log likelihood: -3940.355381
EM: Round [758] log likelihood: -3940.355263
EM: Round [759] log likelihood: -3940.355146
EM: Round [760] log likelihood: -3940.355030
EM: Round [761] log likelihood: -3940.354914
EM: Round [762] log likelihood: -3940.354799
EM: Round [763] log likelihood: -3940.354685
EM: Round [764] log likelihood: -3940.354571
EM: Round [765] log likelihood: -3940.354457
EM: Round [766] log likelihood: -3940.354345
EM: Round [767] log likelihood: -3940.354232
EM: Round [768] log likelihood: -3940.354121
EM: Round [769] log likelihood: -3940.354010
EM: Round [770] log likelihood: -3940.353899
EM: Round [771] log likelihood: -3940.353790
EM: Round [772] log likelihood: -3940.353680
EM: Round [773] log likelihood: -3940.353572
EM: Round [774] log likelihood: -3940.353463
EM: Round [775] log likelihood: -3940.353356
EM: Round [776] log likelihood: -3940.353249
EM: Round [777] log likelihood: -3940.353142
EM: Round [778] log likelihood: -3940.353037
EM: Round [779] log likelihood: -3940.352931
EM: Round [780] log likelihood: -3940.352826
EM: Round [781] log likelihood: -3940.352722
EM: Round [782] log likelihood: -3940.352618
EM: Round [783] log likelihood: -3940.352515
EM: Round [784] log likelihood: -3940.352412
EM: Round [785] log likelihood: -3940.352310
EM: Round [786] log likelihood: -3940.352209
EM: Round [787] log likelihood: -3940.352108
EM: Round [788] log likelihood: -3940.352007
EM: Round [789] log likelihood: -3940.351907
EM: Round [790] log likelihood: -3940.351808
EM: Stopping iterations at round 790 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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa > /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir
-done, see /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -3030.811484
EM: Round [1] log likelihood: -3030.486362
EM: Round [2] log likelihood: -3030.486084
EM: Round [3] log likelihood: -3030.486083
EM: Stopping iterations at round 3 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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 296414775
Execution Time = 5.94 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf  > /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.gtf  > /tmp/nxf.juLjv4mr3C/fi_workdir/microH.dat
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.juLjv4mr3C/fi_workdir/microH.dat /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/fi_workdir/microH.dat /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.juLjv4mr3C --json_outfile /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-b675f7-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.juLjv4mr3C --json_outfile /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-b675f7-R1_A23WJ53LT4_1
Running: touch /tmp/nxf.juLjv4mr3C/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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-b675f7-R1_A23WJ53LT4_1 --html_output /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-b675f7-R1_A23WJ53LT4_1 --html_output /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-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.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000233013.10]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000226824.7]
WARNING, no entry stored in dbm for [ENSG00000226824.7]
WARNING, no entry stored in dbm for [ENSG00000226824.7]
WARNING, no entry stored in dbm for [ENSG00000226824.7]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.juLjv4mr3C/ctat_genome_lib_build_dir > /tmp/nxf.juLjv4mr3C/aih-tih-sc-b675f7-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.juLjv4mr3C/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory