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/30/8e8828768d68cec1e28e71efea6b55/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/8e8828768d68cec1e28e71efea6b55/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/003213e3c2d0cbb9a0e5e7f4ae7162/aih-tih-sc-92d360-R1_A23YTGFLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/8104b4b0ab7c8cc196aedf761ae43a/aih-tih-sc-92d360-R1_A23YTGFLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/003213e3c2d0cbb9a0e5e7f4ae7162/aih-tih-sc-92d360-R1_A23YTGFLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.Jb0EzlqBLb/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.Jb0EzlqBLb/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary
-sample contains 242091830 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.Jb0EzlqBLb/ctat_genome_lib_build_dir  -J /tmp/nxf.Jb0EzlqBLb/aih-tih-sc-92d360-R1_A23YTGFLT4_1.Chimeric.out.junction  -O /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.Jb0EzlqBLb/aih-tih-sc-92d360-R1_A23YTGFLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.Jb0EzlqBLb/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes

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[2160000], rate=65223.96/min -building interval tree based on /tmp/nxf.Jb0EzlqBLb/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes

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[2160000], rate=59613.62/min -building interval tree based on /tmp/nxf.Jb0EzlqBLb/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.13 min).
-mapping reads to genes

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[2120000], rate=48000.00/min 
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[2140000], rate=48035.91/min 
[2150000], rate=48062.59/min 
[2160000], rate=48089.05/min -building interval tree based on /tmp/nxf.Jb0EzlqBLb/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.13 min).
-mapping reads to genes

[10000], rate=66666.67/min 
[20000], rate=70588.24/min 
[30000], rate=90000.00/min 
[40000], rate=114285.71/min 
[50000], rate=136363.64/min 
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[70000], rate=140000.00/min 
[80000], rate=129729.73/min 
[90000], rate=122727.27/min 
[100000], rate=125000.00/min 
[110000], rate=124528.30/min 
[120000], rate=116129.03/min 
[130000], rate=109859.15/min 
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[870000], rate=35582.82/min 
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[1000000], rate=36144.58/min 
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[2000000], rate=44843.05/min 
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[2140000], rate=46673.94/min 
[2150000], rate=46789.99/min 
[2160000], rate=46922.52/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.Jb0EzlqBLb/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 6000000.00 reads per min processed...  
 12000000.00 reads per min processed...  
 9000000.00 reads per min processed...  
 12000000.00 reads per min processed...  
 7500000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 5250000.00 reads per min processed...  
 4800000.00 reads per min processed...  
 4500000.00 reads per min processed...  
 4615384.62 reads per min processed...  
 4400000.00 reads per min processed...  
 4235294.12 reads per min processed...  
 4105263.16 reads per min processed...  
 4000000.00 reads per min processed...  
 4090909.09 reads per min processed...  
 4000000.00 reads per min processed...  
 3923076.92 reads per min processed...  
 3857142.86 reads per min processed...  
 3800000.00 reads per min processed...  
 3750000.00 reads per min processed...  
 3705882.35 reads per min processed...  
 3666666.67 reads per min processed...  
 3631578.95 reads per min processed...  
 3600000.00 reads per min processed...  
 3571428.57 reads per min processed...  
 3545454.55 reads per min processed...  
 3521739.13 reads per min processed...  
 3500000.00 reads per min processed...  
 3480000.00 reads per min processed...  
 3529411.76 reads per min processed...  
 3509433.96 reads per min processed...  
 3490909.09 reads per min processed...  
 3473684.21 reads per min processed...  
 3517241.38 reads per min processed...  
 3500000.00 reads per min processed...  
 3483870.97 reads per min processed...  
 3523809.52 reads per min processed...  
 3507692.31 reads per min processed...  
 3492537.31 reads per min processed...  
 3529411.76 reads per min processed...  
 3565217.39 reads per min processed...  
 3600000.00 reads per min processed...  
 3685714.29 reads per min processed...  
 3718309.86 reads per min processed...  
 3698630.14 reads per min processed...  
 3680000.00 reads per min processed...  
 3710526.32 reads per min processed...  
 3692307.69 reads per min processed...  
 3721518.99 reads per min processed...  
 3703703.70 reads per min processed...  
 3686746.99 reads per min processed...  
 3714285.71 reads per min processed...  
 3697674.42 reads per min processed...  
 3724137.93 reads per min processed...  
 3707865.17 reads per min processed...  
 3692307.69 reads per min processed...  
 3677419.35 reads per min processed...  
 3702127.66 reads per min processed...  
 3687500.00 reads per min processed...  
 3711340.21 reads per min processed...  
 3696969.70 reads per min processed...  
 3683168.32 reads per min processed...  
 3669902.91 reads per min processed...  
 3657142.86 reads per min processed...  
 3679245.28 reads per min processed...  
 3666666.67 reads per min processed...  
 3654545.45 reads per min processed...  
 3675675.68 reads per min processed...  
 3663716.81 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.Jb0EzlqBLb/aih-tih-sc-92d360-R1_A23YTGFLT4_1.Chimeric.out.junction  --tmpdir /tmp  --min_junction_reads 0  --min_sum_frags 1  --require_LDAS 0  --max_promiscuity 10  --min_pct_dom_promiscuity 20  --min_novel_junction_support 1  --min_alt_pct_junction 10  --aggregate_novel_junction_dist 5  --min_spanning_frags_only 1  --genome_lib_dir /tmp/nxf.Jb0EzlqBLb/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.Jb0EzlqBLb/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -602583.088476
EM: Round [1] log likelihood: -602291.107367
EM: Round [2] log likelihood: -602186.245107
EM: Round [3] log likelihood: -602137.981073
EM: Round [4] log likelihood: -602112.967705
EM: Round [5] log likelihood: -602099.165753
EM: Round [6] log likelihood: -602091.184410
EM: Round [7] log likelihood: -602086.352290
EM: Round [8] log likelihood: -602083.287778
EM: Round [9] log likelihood: -602081.255909
EM: Round [10] log likelihood: -602079.853396
EM: Round [11] log likelihood: -602078.850857
EM: Round [12] log likelihood: -602078.112703
EM: Round [13] log likelihood: -602077.555618
EM: Round [14] log likelihood: -602077.126462
EM: Round [15] log likelihood: -602076.790140
EM: Round [16] log likelihood: -602076.522736
EM: Round [17] log likelihood: -602076.307492