Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/e803a4d08a61acca244481e285871e/659_w_T1_TRNA_1_B2372Y3LT4_1.Chimeric.out.junction
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/ba/0efbf5e80c4ea02b478560ad21e2d9/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/0efbf5e80c4ea02b478560ad21e2d9/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/bc4bf63a91d70bf8ec0c7e4986a53b/659_w_T1_TRNA_1_B2372Y3LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/bc4bf63a91d70bf8ec0c7e4986a53b/659_w_T1_TRNA_1_B2372Y3LT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.ySzU6DZ3pB/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.ySzU6DZ3pB/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary
-sample contains 101046404 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.ySzU6DZ3pB/ctat_genome_lib_build_dir -J /tmp/nxf.ySzU6DZ3pB/659_w_T1_TRNA_1_B2372Y3LT4_1.Chimeric.out.junction -O /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.ySzU6DZ3pB/659_w_T1_TRNA_1_B2372Y3LT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.ySzU6DZ3pB/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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[990000], rate=90964.78/min -building interval tree based on /tmp/nxf.ySzU6DZ3pB/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
[10000], rate=200000.00/min
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[980000], rate=71619.98/min -building interval tree based on /tmp/nxf.ySzU6DZ3pB/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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[980000], rate=63636.36/min -building interval tree based on /tmp/nxf.ySzU6DZ3pB/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
[10000], rate=33333.33/min
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[980000], rate=60806.62/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.ySzU6DZ3pB/ctat_genome_lib_build_dir --filt_file /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.ySzU6DZ3pB/./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...
18000000.00 reads per min processed...
12000000.00 reads per min processed...
10000000.00 reads per min processed...
7200000.00 reads per min processed...
6000000.00 reads per min processed...
5333333.33 reads per min processed...
4909090.91 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...
3913043.48 reads per min processed...
3840000.00 reads per min processed...
3777777.78 reads per min processed...
3857142.86 reads per min processed...
3800000.00 reads per min processed...
3870967.74 reads per min processed...
3937500.00 reads per min processed...
4125000.00 reads per min processed...
4181818.18 reads per min processed...
4235294.12 reads per min processed...
4166666.67 reads per min processed...
4105263.16 reads per min processed...
4153846.15 reads per min processed...
4097560.98 reads per min processed...
4046511.63 reads per min processed...
4000000.00 reads per min processed...
3957446.81 reads per min processed...
3918367.35 reads per min processed...
3960000.00 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.ySzU6DZ3pB/659_w_T1_TRNA_1_B2372Y3LT4_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.ySzU6DZ3pB/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -230098.111991
EM: Round [1] log likelihood: -229959.418128
EM: Round [2] log likelihood: -229914.274896
EM: Round [3] log likelihood: -229893.645581
EM: Round [4] log likelihood: -229882.726949
EM: Round [5] log likelihood: -229876.487757
EM: Round [6] log likelihood: -229872.715559
EM: Round [7] log likelihood: -229870.314682
EM: Round [8] log likelihood: -229868.711663
EM: Round [9] log likelihood: -229867.594485
EM: Round [10] log likelihood: -229866.786810
EM: Round [11] log likelihood: -229866.184873
EM: Round [12] log likelihood: -229865.725019
EM: Round [13] log likelihood: -229865.366585
EM: Round [14] log likelihood: -229865.082600
EM: Round [15] log likelihood: -229864.854560
EM: Round [16] log likelihood: -229864.669390
EM: Round [17] log likelihood: -229864.517615
EM: Round [18] log likelihood: -229864.392214
EM: Round [19] log likelihood: -229864.287892
EM: Round [20] log likelihood: -229864.200586
EM: Round [21] log likelihood: -229864.127138
EM: Round [22] log likelihood: -229864.065062
EM: Round [23] log likelihood: -229864.012381
EM: Round [24] log likelihood: -229863.967507
EM: Round [25] log likelihood: -229863.929156
EM: Round [26] log likelihood: -229863.896279
EM: Round [27] log likelihood: -229863.868016
EM: Round [28] log likelihood: -229863.843656
EM: Round [29] log likelihood: -229863.822611
EM: Round [30] log likelihood: -229863.804388
EM: Round [31] log likelihood: -229863.788575
EM: Round [32] log likelihood: -229863.774826
EM: Round [33] log likelihood: -229863.762849
EM: Round [34] log likelihood: -229863.752395
EM: Round [35] log likelihood: -229863.743256
EM: Round [36] log likelihood: -229863.735251
EM: Round [37] log likelihood: -229863.728229
EM: Round [38] log likelihood: -229863.722059
EM: Round [39] log likelihood: -229863.716629
EM: Round [40] log likelihood: -229863.711842
EM: Round [41] log likelihood: -229863.707617
EM: Round [42] log likelihood: -229863.703881
EM: Round [43] log likelihood: -229863.700573
EM: Round [44] log likelihood: -229863.697639
EM: Round [45] log likelihood: -229863.695034
EM: Round [46] log likelihood: -229863.692718
EM: Round [47] log likelihood: -229863.690654
EM: Round [48] log likelihood: -229863.688814
EM: Round [49] log likelihood: -229863.687171
EM: Round [50] log likelihood: -229863.685701
EM: Round [51] log likelihood: -229863.684385
EM: Round [52] log likelihood: -229863.683204
EM: Round [53] log likelihood: -229863.682144
EM: Round [54] log likelihood: -229863.681190
EM: Round [55] log likelihood: -229863.680332
EM: Round [56] log likelihood: -229863.679557
EM: Round [57] log likelihood: -229863.678858
EM: Round [58] log likelihood: -229863.678226
EM: Round [59] log likelihood: -229863.677653
EM: Round [60] log likelihood: -229863.677134
EM: Round [61] log likelihood: -229863.676663
EM: Round [62] log likelihood: -229863.676234
EM: Round [63] log likelihood: -229863.675844
EM: Round [64] log likelihood: -229863.675489
EM: Round [65] log likelihood: -229863.675164
EM: Round [66] log likelihood: -229863.674867
EM: Round [67] log likelihood: -229863.674596
EM: Round [68] log likelihood: -229863.674347
EM: Round [69] log likelihood: -229863.674118
EM: Round [70] log likelihood: -229863.673908
EM: Round [71] log likelihood: -229863.673715
EM: Round [72] log likelihood: -229863.673537
EM: Round [73] log likelihood: -229863.673372
EM: Round [74] log likelihood: -229863.673220
EM: Round [75] log likelihood: -229863.673079
EM: Round [76] log likelihood: -229863.672949
EM: Round [77] log likelihood: -229863.672828
EM: Round [78] log likelihood: -229863.672715
EM: Round [79] log likelihood: -229863.672610
EM: Round [80] log likelihood: -229863.672513
EM: Stopping iterations at round 80 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -229556.160811
EM: Round [1] log likelihood: -229438.445738
EM: Round [2] log likelihood: -229400.971256
EM: Round [3] log likelihood: -229384.253009
EM: Round [4] log likelihood: -229375.583063
EM: Round [5] log likelihood: -229370.718605
EM: Round [6] log likelihood: -229367.827015
EM: Round [7] log likelihood: -229366.014557
EM: Round [8] log likelihood: -229364.820131
EM: Round [9] log likelihood: -229363.996438
EM: Round [10] log likelihood: -229363.405736
EM: Round [11] log likelihood: -229362.968118
EM: Round [12] log likelihood: -229362.635224
EM: Round [13] log likelihood: -229362.376533
EM: Round [14] log likelihood: -229362.172010
EM: Round [15] log likelihood: -229362.008033
EM: Round [16] log likelihood: -229361.875044
EM: Round [17] log likelihood: -229361.766152
EM: Round [18] log likelihood: -229361.676276
EM: Round [19] log likelihood: -229361.601589
EM: Round [20] log likelihood: -229361.539163
EM: Round [21] log likelihood: -229361.486723
EM: Round [22] log likelihood: -229361.442478
EM: Round [23] log likelihood: -229361.405004
EM: Round [24] log likelihood: -229361.373155
EM: Round [25] log likelihood: -229361.346003
EM: Round [26] log likelihood: -229361.322792
EM: Round [27] log likelihood: -229361.302898
EM: Round [28] log likelihood: -229361.285809
EM: Round [29] log likelihood: -229361.271095
EM: Round [30] log likelihood: -229361.258402
EM: Round [31] log likelihood: -229361.247429
EM: Round [32] log likelihood: -229361.237927
EM: Round [33] log likelihood: -229361.229683
EM: Round [34] log likelihood: -229361.222518
EM: Round [35] log likelihood: -229361.216281
EM: Round [36] log likelihood: -229361.210842
EM: Round [37] log likelihood: -229361.206091
EM: Round [38] log likelihood: -229361.201934
EM: Round [39] log likelihood: -229361.198291
EM: Round [40] log likelihood: -229361.195094
EM: Round [41] log likelihood: -229361.192282
EM: Round [42] log likelihood: -229361.189807
EM: Round [43] log likelihood: -229361.187623
EM: Round [44] log likelihood: -229361.185693
EM: Round [45] log likelihood: -229361.183985
EM: Round [46] log likelihood: -229361.182471
EM: Round [47] log likelihood: -229361.181127
EM: Round [48] log likelihood: -229361.179931
EM: Round [49] log likelihood: -229361.178865
EM: Round [50] log likelihood: -229361.177913
EM: Round [51] log likelihood: -229361.177063
EM: Round [52] log likelihood: -229361.176301
EM: Round [53] log likelihood: -229361.175617
EM: Round [54] log likelihood: -229361.175002
EM: Round [55] log likelihood: -229361.174448
EM: Round [56] log likelihood: -229361.173949
EM: Round [57] log likelihood: -229361.173497
EM: Round [58] log likelihood: -229361.173089
EM: Round [59] log likelihood: -229361.172718
EM: Round [60] log likelihood: -229361.172381
EM: Round [61] log likelihood: -229361.172075
EM: Round [62] log likelihood: -229361.171795
EM: Round [63] log likelihood: -229361.171539
EM: Round [64] log likelihood: -229361.171306
EM: Round [65] log likelihood: -229361.171091
EM: Round [66] log likelihood: -229361.170894
EM: Round [67] log likelihood: -229361.170713
EM: Round [68] log likelihood: -229361.170546
EM: Round [69] log likelihood: -229361.170392
EM: Round [70] log likelihood: -229361.170250
EM: Round [71] log likelihood: -229361.170118
EM: Round [72] log likelihood: -229361.169995
EM: Round [73] log likelihood: -229361.169882
EM: Round [74] log likelihood: -229361.169776
EM: Round [75] log likelihood: -229361.169677
EM: Stopping iterations at round 75 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ySzU6DZ3pB/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ySzU6DZ3pB/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ySzU6DZ3pB/ctat_genome_lib_build_dir