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/e9/396e67095bcdb706209041294bd4c3/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/bc00b8bd4961ec79badbb39c1b49bf/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/396e67095bcdb706209041294bd4c3/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/98d524084eee26e62db9b60d473325/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/98d524084eee26e62db9b60d473325/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.s3HI74ZYeN/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary
-sample contains 81322568 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir -J /tmp/nxf.s3HI74ZYeN/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction -O /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.s3HI74ZYeN/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction
-building interval tree based on /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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[1630000], rate=79706.60/min -building interval tree based on /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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[1620000], rate=73916.35/min -building interval tree based on /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes
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[1620000], rate=72591.49/min -building interval tree based on /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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[230000], rate=166265.06/min
[240000], rate=158241.76/min
[250000], rate=159574.47/min
[260000], rate=160824.74/min
[270000], rate=163636.36/min
[280000], rate=163106.80/min
[290000], rate=162616.82/min
[300000], rate=165137.61/min
[310000], rate=170642.20/min
[320000], rate=174545.45/min
[330000], rate=176785.71/min
[340000], rate=174358.97/min
[350000], rate=172131.15/min
[360000], rate=168750.00/min
[370000], rate=168181.82/min
[380000], rate=167647.06/min
[390000], rate=167142.86/min
[400000], rate=170212.77/min
[410000], rate=172027.97/min
[420000], rate=169127.52/min
[430000], rate=163291.14/min
[440000], rate=160975.61/min
[450000], rate=158823.53/min
[460000], rate=158620.69/min
[470000], rate=160227.27/min
[480000], rate=160000.00/min
[490000], rate=158918.92/min
[500000], rate=159574.47/min
[510000], rate=159375.00/min
[520000], rate=157575.76/min
[530000], rate=155121.95/min
[540000], rate=153554.50/min
[550000], rate=154205.61/min
[560000], rate=153424.66/min
[570000], rate=154751.13/min
[580000], rate=156053.81/min
[590000], rate=155947.14/min
[600000], rate=153846.15/min
[610000], rate=151239.67/min
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[640000], rate=152988.05/min
[650000], rate=152343.75/min
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[680000], rate=147826.09/min
[690000], rate=128173.37/min
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[710000], rate=114516.13/min
[720000], rate=109644.67/min
[730000], rate=105288.46/min
[740000], rate=101601.83/min
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[760000], rate=95000.00/min
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[780000], rate=90173.41/min
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[820000], rate=82689.08/min
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[870000], rate=78026.91/min
[880000], rate=77533.04/min
[890000], rate=77056.28/min
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[1310000], rate=74291.12/min
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[1380000], rate=72887.32/min
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[1430000], rate=72040.30/min
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[1510000], rate=72538.03/min
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[1540000], rate=72985.78/min
[1550000], rate=72884.01/min
[1560000], rate=72727.27/min
[1570000], rate=72517.32/min
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[1600000], rate=72180.45/min
[1610000], rate=72143.39/min
[1620000], rate=72106.82/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir --filt_file /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
0.00 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...
12000000.00 reads per min processed...
8400000.00 reads per min processed...
8000000.00 reads per min processed...
6750000.00 reads per min processed...
6666666.67 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
5625000.00 reads per min processed...
5647058.82 reads per min processed...
5666666.67 reads per min processed...
5400000.00 reads per min processed...
5428571.43 reads per min processed...
5217391.30 reads per min processed...
5250000.00 reads per min processed...
5076923.08 reads per min processed...
4928571.43 reads per min processed...
4965517.24 reads per min processed...
4838709.68 reads per min processed...
4875000.00 reads per min processed...
4909090.91 reads per min processed...
4941176.47 reads per min processed...
4833333.33 reads per min processed...
4864864.86 reads per min processed...
4894736.84 reads per min processed...
4923076.92 reads per min processed...
4950000.00 reads per min processed...
4857142.86 reads per min processed...
4883720.93 reads per min processed...
4909090.91 reads per min processed...
5045454.55 reads per min processed...
5066666.67 reads per min processed...
5200000.00 reads per min processed...
5217391.30 reads per min processed...
5234042.55 reads per min processed...
5142857.14 reads per min processed...
5160000.00 reads per min processed...
5176470.59 reads per min processed...
5192307.69 reads per min processed...
5207547.17 reads per min processed...
5127272.73 reads per min processed...
5142857.14 reads per min processed...
5157894.74 reads per min processed...
5084745.76 reads per min processed...
5100000.00 reads per min processed...
5032258.06 reads per min processed...
5047619.05 reads per min processed...
5062500.00 reads per min processed...
5076923.08 reads per min processed...
5090909.09 reads per min processed...
5104477.61 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.s3HI74ZYeN/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.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.s3HI74ZYeN/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -113244.124138
EM: Round [1] log likelihood: -113023.491463
EM: Round [2] log likelihood: -112935.451184
EM: Round [3] log likelihood: -112892.471482
EM: Round [4] log likelihood: -112869.735161
EM: Round [5] log likelihood: -112857.132953
EM: Round [6] log likelihood: -112849.860312
EM: Round [7] log likelihood: -112845.488208
EM: Round [8] log likelihood: -112842.749437
EM: Round [9] log likelihood: -112840.964653
EM: Round [10] log likelihood: -112839.758398
EM: Round [11] log likelihood: -112838.916077
EM: Round [12] log likelihood: -112838.310688
EM: Round [13] log likelihood: -112837.864442
EM: Round [14] log likelihood: -112837.528117
EM: Round [15] log likelihood: -112837.269623
EM: Round [16] log likelihood: -112837.067464
EM: Round [17] log likelihood: -112836.906890
EM: Round [18] log likelihood: -112836.777558
EM: Round [19] log likelihood: -112836.672077
EM: Round [20] log likelihood: -112836.585070
EM: Round [21] log likelihood: -112836.512563
EM: Round [22] log likelihood: -112836.451579
EM: Round [23] log likelihood: -112836.399854
EM: Round [24] log likelihood: -112836.355647
EM: Round [25] log likelihood: -112836.317604
EM: Round [26] log likelihood: -112836.284658
EM: Round [27] log likelihood: -112836.255962
EM: Round [28] log likelihood: -112836.230835
EM: Round [29] log likelihood: -112836.208728
EM: Round [30] log likelihood: -112836.189190
EM: Round [31] log likelihood: -112836.171852
EM: Round [32] log likelihood: -112836.156407
EM: Round [33] log likelihood: -112836.142601
EM: Round [34] log likelihood: -112836.130218
EM: Round [35] log likelihood: -112836.119078
EM: Round [36] log likelihood: -112836.109027
EM: Round [37] log likelihood: -112836.099935
EM: Round [38] log likelihood: -112836.091688
EM: Round [39] log likelihood: -112836.084190
EM: Round [40] log likelihood: -112836.077358
EM: Round [41] log likelihood: -112836.071119
EM: Round [42] log likelihood: -112836.065411
EM: Round [43] log likelihood: -112836.060176
EM: Round [44] log likelihood: -112836.055368
EM: Round [45] log likelihood: -112836.050944
EM: Round [46] log likelihood: -112836.046866
EM: Round [47] log likelihood: -112836.043101
EM: Round [48] log likelihood: -112836.039619
EM: Round [49] log likelihood: -112836.036394
EM: Round [50] log likelihood: -112836.033403
EM: Round [51] log likelihood: -112836.030625
EM: Round [52] log likelihood: -112836.028041
EM: Round [53] log likelihood: -112836.025635
EM: Round [54] log likelihood: -112836.023391
EM: Round [55] log likelihood: -112836.021296
EM: Round [56] log likelihood: -112836.019337
EM: Round [57] log likelihood: -112836.017504
EM: Round [58] log likelihood: -112836.015786
EM: Round [59] log likelihood: -112836.014174
EM: Round [60] log likelihood: -112836.012661
EM: Round [61] log likelihood: -112836.011238
EM: Round [62] log likelihood: -112836.009899
EM: Round [63] log likelihood: -112836.008638
EM: Round [64] log likelihood: -112836.007448
EM: Round [65] log likelihood: -112836.006326
EM: Round [66] log likelihood: -112836.005265
EM: Round [67] log likelihood: -112836.004262
EM: Round [68] log likelihood: -112836.003312
EM: Round [69] log likelihood: -112836.002413
EM: Round [70] log likelihood: -112836.001560
EM: Round [71] log likelihood: -112836.000751
EM: Round [72] log likelihood: -112835.999982
EM: Round [73] log likelihood: -112835.999252
EM: Round [74] log likelihood: -112835.998557
EM: Round [75] log likelihood: -112835.997895
EM: Round [76] log likelihood: -112835.997265
EM: Round [77] log likelihood: -112835.996664
EM: Round [78] log likelihood: -112835.996091
EM: Round [79] log likelihood: -112835.995544
EM: Round [80] log likelihood: -112835.995022
EM: Round [81] log likelihood: -112835.994522
EM: Round [82] log likelihood: -112835.994045
EM: Round [83] log likelihood: -112835.993588
EM: Round [84] log likelihood: -112835.993150
EM: Round [85] log likelihood: -112835.992730
EM: Round [86] log likelihood: -112835.992328
EM: Round [87] log likelihood: -112835.991943
EM: Round [88] log likelihood: -112835.991573
EM: Round [89] log likelihood: -112835.991217
EM: Round [90] log likelihood: -112835.990876
EM: Round [91] log likelihood: -112835.990548
EM: Round [92] log likelihood: -112835.990233
EM: Round [93] log likelihood: -112835.989929
EM: Round [94] log likelihood: -112835.989637
EM: Round [95] log likelihood: -112835.989356
EM: Round [96] log likelihood: -112835.989085
EM: Round [97] log likelihood: -112835.988825
EM: Round [98] log likelihood: -112835.988573
EM: Round [99] log likelihood: -112835.988331
EM: Round [100] log likelihood: -112835.988097
EM: Round [101] log likelihood: -112835.987871
EM: Round [102] log likelihood: -112835.987653
EM: Round [103] log likelihood: -112835.987443
EM: Round [104] log likelihood: -112835.987240
EM: Round [105] log likelihood: -112835.987044
EM: Round [106] log likelihood: -112835.986854
EM: Round [107] log likelihood: -112835.986670
EM: Round [108] log likelihood: -112835.986493
EM: Round [109] log likelihood: -112835.986322
EM: Round [110] log likelihood: -112835.986156
EM: Round [111] log likelihood: -112835.985995
EM: Round [112] log likelihood: -112835.985839
EM: Round [113] log likelihood: -112835.985689
EM: Round [114] log likelihood: -112835.985543
EM: Round [115] log likelihood: -112835.985401
EM: Round [116] log likelihood: -112835.985264
EM: Round [117] log likelihood: -112835.985132
EM: Round [118] log likelihood: -112835.985003
EM: Round [119] log likelihood: -112835.984878
EM: Round [120] log likelihood: -112835.984757
EM: Round [121] log likelihood: -112835.984640
EM: Round [122] log likelihood: -112835.984526
EM: Round [123] log likelihood: -112835.984415
EM: Round [124] log likelihood: -112835.984308
EM: Round [125] log likelihood: -112835.984203
EM: Round [126] log likelihood: -112835.984102
EM: Round [127] log likelihood: -112835.984004
EM: Stopping iterations at round 127 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -113141.240086
EM: Round [1] log likelihood: -112959.154590
EM: Round [2] log likelihood: -112890.907775
EM: Round [3] log likelihood: -112858.415537
EM: Round [4] log likelihood: -112841.399922
EM: Round [5] log likelihood: -112832.007118
EM: Round [6] log likelihood: -112826.599668
EM: Round [7] log likelihood: -112823.357972
EM: Round [8] log likelihood: -112821.335763
EM: Round [9] log likelihood: -112820.025673
EM: Round [10] log likelihood: -112819.146919
EM: Round [11] log likelihood: -112818.538795
EM: Round [12] log likelihood: -112818.106118
EM: Round [13] log likelihood: -112817.790605
EM: Round [14] log likelihood: -112817.555430
EM: Round [15] log likelihood: -112817.376651
EM: Round [16] log likelihood: -112817.238299
EM: Round [17] log likelihood: -112817.129479
EM: Round [18] log likelihood: -112817.042604
EM: Round [19] log likelihood: -112816.972297
EM: Round [20] log likelihood: -112816.914682
EM: Round [21] log likelihood: -112816.866926
EM: Round [22] log likelihood: -112816.826927
EM: Round [23] log likelihood: -112816.793103
EM: Round [24] log likelihood: -112816.764255
EM: Round [25] log likelihood: -112816.739457
EM: Round [26] log likelihood: -112816.717987
EM: Round [27] log likelihood: -112816.699279
EM: Round [28] log likelihood: -112816.682882
EM: Round [29] log likelihood: -112816.668434
EM: Round [30] log likelihood: -112816.655641
EM: Round [31] log likelihood: -112816.644263
EM: Round [32] log likelihood: -112816.634102
EM: Round [33] log likelihood: -112816.624994
EM: Round [34] log likelihood: -112816.616801
EM: Round [35] log likelihood: -112816.609408
EM: Round [36] log likelihood: -112816.602716
EM: Round [37] log likelihood: -112816.596641
EM: Round [38] log likelihood: -112816.591113
EM: Round [39] log likelihood: -112816.586069
EM: Round [40] log likelihood: -112816.581456
EM: Round [41] log likelihood: -112816.577228
EM: Round [42] log likelihood: -112816.573344
EM: Round [43] log likelihood: -112816.569770
EM: Round [44] log likelihood: -112816.566473
EM: Round [45] log likelihood: -112816.563427
EM: Round [46] log likelihood: -112816.560607
EM: Round [47] log likelihood: -112816.557992
EM: Round [48] log likelihood: -112816.555564
EM: Round [49] log likelihood: -112816.553304
EM: Round [50] log likelihood: -112816.551199
EM: Round [51] log likelihood: -112816.549234
EM: Round [52] log likelihood: -112816.547398
EM: Round [53] log likelihood: -112816.545679
EM: Round [54] log likelihood: -112816.544069
EM: Round [55] log likelihood: -112816.542557
EM: Round [56] log likelihood: -112816.541136
EM: Round [57] log likelihood: -112816.539800
EM: Round [58] log likelihood: -112816.538541
EM: Round [59] log likelihood: -112816.537353
EM: Round [60] log likelihood: -112816.536232
EM: Round [61] log likelihood: -112816.535171
EM: Round [62] log likelihood: -112816.534168
EM: Round [63] log likelihood: -112816.533218
EM: Round [64] log likelihood: -112816.532316
EM: Round [65] log likelihood: -112816.531460
EM: Round [66] log likelihood: -112816.530647
EM: Round [67] log likelihood: -112816.529874
EM: Round [68] log likelihood: -112816.529138
EM: Round [69] log likelihood: -112816.528436
EM: Round [70] log likelihood: -112816.527768
EM: Round [71] log likelihood: -112816.527129
EM: Round [72] log likelihood: -112816.526520
EM: Round [73] log likelihood: -112816.525937
EM: Round [74] log likelihood: -112816.525380
EM: Round [75] log likelihood: -112816.524846
EM: Round [76] log likelihood: -112816.524336
EM: Round [77] log likelihood: -112816.523846
EM: Round [78] log likelihood: -112816.523376
EM: Round [79] log likelihood: -112816.522926
EM: Round [80] log likelihood: -112816.522493
EM: Round [81] log likelihood: -112816.522078
EM: Round [82] log likelihood: -112816.521678
EM: Round [83] log likelihood: -112816.521294
EM: Round [84] log likelihood: -112816.520924
EM: Round [85] log likelihood: -112816.520568
EM: Round [86] log likelihood: -112816.520226
EM: Round [87] log likelihood: -112816.519895
EM: Round [88] log likelihood: -112816.519577
EM: Round [89] log likelihood: -112816.519270
EM: Round [90] log likelihood: -112816.518974
EM: Round [91] log likelihood: -112816.518688
EM: Round [92] log likelihood: -112816.518413
EM: Round [93] log likelihood: -112816.518146
EM: Round [94] log likelihood: -112816.517889
EM: Round [95] log likelihood: -112816.517640
EM: Round [96] log likelihood: -112816.517400
EM: Round [97] log likelihood: -112816.517167
EM: Round [98] log likelihood: -112816.516943
EM: Round [99] log likelihood: -112816.516725
EM: Round [100] log likelihood: -112816.516515
EM: Round [101] log likelihood: -112816.516311
EM: Round [102] log likelihood: -112816.516113
EM: Round [103] log likelihood: -112816.515922
EM: Round [104] log likelihood: -112816.515737
EM: Round [105] log likelihood: -112816.515558
EM: Round [106] log likelihood: -112816.515384
EM: Round [107] log likelihood: -112816.515215
EM: Round [108] log likelihood: -112816.515052
EM: Round [109] log likelihood: -112816.514894
EM: Round [110] log likelihood: -112816.514740
EM: Round [111] log likelihood: -112816.514591
EM: Round [112] log likelihood: -112816.514446
EM: Round [113] log likelihood: -112816.514306
EM: Round [114] log likelihood: -112816.514169
EM: Round [115] log likelihood: -112816.514037
EM: Round [116] log likelihood: -112816.513909
EM: Round [117] log likelihood: -112816.513784
EM: Round [118] log likelihood: -112816.513663
EM: Round [119] log likelihood: -112816.513545
EM: Round [120] log likelihood: -112816.513430
EM: Round [121] log likelihood: -112816.513319
EM: Round [122] log likelihood: -112816.513211
EM: Round [123] log likelihood: -112816.513106
EM: Round [124] log likelihood: -112816.513004
EM: Round [125] log likelihood: -112816.512905
EM: Stopping iterations at round 125 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter
CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered
* Running CMD: /usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 81322568 > /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM
* Running CMD: /usr/local/src/STAR-Fusion/util/append_breakpoint_junction_info.pl /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir > /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir --annotate /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot
* Running CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir
-done, see /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_likely_RT_artifacts.pl --fusions /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 522, filtered: 6515)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.s3HI74ZYeN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass.minFFPM.0.00001.pass star-fusion.fusion_predictions.tsv
* Running CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl star-fusion.fusion_predictions.tsv JunctionReads,SpanningFrags > star-fusion.fusion_predictions.abridged.tsv
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions star-fusion.fusion_predictions.abridged.tsv --genome_lib_dir /tmp/nxf.s3HI74ZYeN/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000229739.4]
WARNING, no entry stored in dbm for [ENSG00000234715.2]
WARNING, no entry stored in dbm for [ENSG00000205312.8]
WARNING, no entry stored in dbm for [ENSG00000280383.1]
WARNING, no entry stored in dbm for [ENSG00000286511.1]
WARNING, no entry stored in dbm for [ENSG00000233290.3]
WARNING, no entry stored in dbm for [ENSG00000216352.1]
WARNING, no entry stored in dbm for [ENSG00000233325.3]
WARNING, no entry stored in dbm for [ENSG00000254951.7]
WARNING, no entry stored in dbm for [ENSG00000180458.2]
WARNING, no entry stored in dbm for [ENSG00000241015.2]
WARNING, no entry stored in dbm for [ENSG00000264920.2]
WARNING, no entry stored in dbm for [ENSG00000177410.13]
WARNING, no entry stored in dbm for [ENSG00000263527.1]
WARNING, no entry stored in dbm for [ENSG00000229124.7]
WARNING, no entry stored in dbm for [ENSG00000159247.13]
WARNING, no entry stored in dbm for [ENSG00000223429.1]
WARNING, no entry stored in dbm for [ENSG00000258471.2]
WARNING, no entry stored in dbm for [ENSG00000231058.1]
WARNING, no entry stored in dbm for [ENSG00000257210.1]
WARNING, no entry stored in dbm for [ENSG00000236107.10]
WARNING, no entry stored in dbm for [ENSG00000264589.4]
WARNING, no entry stored in dbm for [ENSG00000261126.7]
WARNING, no entry stored in dbm for [ENSG00000280007.1]
WARNING, no entry stored in dbm for [ENSG00000236200.6]
WARNING, no entry stored in dbm for [ENSG00000225637.1]
WARNING, no entry stored in dbm for [ENSG00000241286.2]
WARNING, no entry stored in dbm for [ENSG00000233565.1]
WARNING, no entry stored in dbm for [ENSG00000243964.1]
WARNING, no entry stored in dbm for [ENSG00000213122.4]
WARNING, no entry stored in dbm for [ENSG00000236148.5]
WARNING, no entry stored in dbm for [ENSG00000230370.1]
WARNING, no entry stored in dbm for [ENSG00000207357.1]
WARNING, no entry stored in dbm for [ENSG00000263934.5]
WARNING, no entry stored in dbm for [ENSG00000243562.3]
WARNING, no entry stored in dbm for [ENSG00000244732.3]
WARNING, no entry stored in dbm for [ENSG00000244056.3]
WARNING, no entry stored in dbm for [ENSG00000239437.3]
WARNING, no entry stored in dbm for [ENSG00000244642.3]
WARNING, no entry stored in dbm for [ENSG00000240106.2]
WARNING, no entry stored in dbm for [ENSG00000244642.3]
WARNING, no entry stored in dbm for [ENSG00000207269.1]
WARNING, no entry stored in dbm for [ENSG00000201201.1]
WARNING, no entry stored in dbm for [ENSG00000259230.1]
WARNING, no entry stored in dbm for [ENSG00000215231.8]
WARNING, no entry stored in dbm for [ENSG00000235438.7]
WARNING, no entry stored in dbm for [ENSG00000227115.8]
WARNING, no entry stored in dbm for [ENSG00000268062.1]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000230461.9]
WARNING, no entry stored in dbm for [ENSG00000259948.2]
WARNING, no entry stored in dbm for [ENSG00000161643.13]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000233705.7]
WARNING, no entry stored in dbm for [ENSG00000255980.1]
WARNING, no entry stored in dbm for [ENSG00000229619.4]
WARNING, no entry stored in dbm for [ENSG00000287810.1]
WARNING, no entry stored in dbm for [ENSG00000236501.6]
WARNING, no entry stored in dbm for [ENSG00000284914.1]
WARNING, no entry stored in dbm for [ENSG00000244479.7]
WARNING, no entry stored in dbm for [ENSG00000204959.4]
WARNING, no entry stored in dbm for [ENSG00000259374.2]
WARNING, no entry stored in dbm for [ENSG00000259374.2]
WARNING, no entry stored in dbm for [ENSG00000277047.5]
WARNING, no entry stored in dbm for [ENSG00000215866.8]
WARNING, no entry stored in dbm for [ENSG00000287721.1]
WARNING, no entry stored in dbm for [ENSG00000244471.6]
WARNING, no entry stored in dbm for [ENSG00000226673.2]
WARNING, no entry stored in dbm for [ENSG00000237076.1]
WARNING, no entry stored in dbm for [ENSG00000261286.1]
WARNING, no entry stored in dbm for [ENSG00000254934.5]
WARNING, no entry stored in dbm for [ENSG00000285462.1]
WARNING, no entry stored in dbm for [ENSG00000286733.1]
WARNING, no entry stored in dbm for [ENSG00000231721.7]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000224699.9]
WARNING, no entry stored in dbm for [ENSG00000259489.2]
WARNING, no entry stored in dbm for [ENSG00000253866.1]
WARNING, no entry stored in dbm for [ENSG00000272913.1]
WARNING, no entry stored in dbm for [ENSG00000254871.1]
WARNING, no entry stored in dbm for [ENSG00000281778.1]
WARNING, no entry stored in dbm for [ENSG00000261457.3]
WARNING, no entry stored in dbm for [ENSG00000214433.4]
WARNING, no entry stored in dbm for [ENSG00000281392.2]
WARNING, no entry stored in dbm for [ENSG00000248265.2]
WARNING, no entry stored in dbm for [ENSG00000236567.2]
WARNING, no entry stored in dbm for [ENSG00000243319.7]
WARNING, no entry stored in dbm for [ENSG00000229231.1]
WARNING, no entry stored in dbm for [ENSG00000232860.8]
WARNING, no entry stored in dbm for [ENSG00000225393.1]
WARNING, no entry stored in dbm for [ENSG00000234690.7]
WARNING, no entry stored in dbm for [ENSG00000182912.6]
WARNING, no entry stored in dbm for [ENSG00000226688.7]
WARNING, no entry stored in dbm for [ENSG00000263883.1]
WARNING, no entry stored in dbm for [ENSG00000232811.1]
WARNING, no entry stored in dbm for [ENSG00000279971.1]
WARNING, no entry stored in dbm for [ENSG00000233937.7]
WARNING, no entry stored in dbm for [ENSG00000279973.2]
WARNING, no entry stored in dbm for [ENSG00000233937.7]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000233937.7]
WARNING, no entry stored in dbm for [ENSG00000248103.1]
WARNING, no entry stored in dbm for [ENSG00000205853.12]
WARNING, no entry stored in dbm for [ENSG00000283541.1]
WARNING, no entry stored in dbm for [ENSG00000268189.2]
WARNING, no entry stored in dbm for [ENSG00000228221.6]
WARNING, no entry stored in dbm for [ENSG00000224809.2]
WARNING, no entry stored in dbm for [ENSG00000235510.1]
WARNING, no entry stored in dbm for [ENSG00000185710.9]
WARNING, no entry stored in dbm for [ENSG00000287586.1]
WARNING, no entry stored in dbm for [ENSG00000279631.1]
WARNING, no entry stored in dbm for [ENSG00000276185.1]
WARNING, no entry stored in dbm for [ENSG00000250838.1]
WARNING, no entry stored in dbm for [ENSG00000230223.8]
WARNING, no entry stored in dbm for [ENSG00000244198.7]
WARNING, no entry stored in dbm for [ENSG00000186466.5]
WARNING, no entry stored in dbm for [ENSG00000254573.1]
WARNING, no entry stored in dbm for [ENSG00000256462.1]
WARNING, no entry stored in dbm for [ENSG00000240291.1]
WARNING, no entry stored in dbm for [ENSG00000273481.1]
WARNING, no entry stored in dbm for [ENSG00000275503.1]
WARNING, no entry stored in dbm for [ENSG00000177788.6]
WARNING, no entry stored in dbm for [ENSG00000286117.2]
WARNING, no entry stored in dbm for [ENSG00000285205.2]
WARNING, no entry stored in dbm for [ENSG00000230922.1]
WARNING, no entry stored in dbm for [ENSG00000261819.1]
WARNING, no entry stored in dbm for [ENSG00000229890.1]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000254319.6]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000261810.1]
WARNING, no entry stored in dbm for [ENSG00000287090.1]
WARNING, no entry stored in dbm for [ENSG00000279048.1]
WARNING, no entry stored in dbm for [ENSG00000254951.7]
WARNING, no entry stored in dbm for [ENSG00000250748.6]
WARNING, no entry stored in dbm for [ENSG00000258419.1]
WARNING, no entry stored in dbm for [ENSG00000231409.3]
WARNING, no entry stored in dbm for [ENSG00000240366.1]
WARNING, no entry stored in dbm for [ENSG00000278972.1]
WARNING, no entry stored in dbm for [ENSG00000288585.1]
WARNING, no entry stored in dbm for [ENSG00000248560.1]
WARNING, no entry stored in dbm for [ENSG00000274525.1]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000274525.1]
WARNING, no entry stored in dbm for [ENSG00000248103.1]
WARNING, no entry stored in dbm for [ENSG00000233397.3]
WARNING, no entry stored in dbm for [ENSG00000239809.1]
WARNING, no entry stored in dbm for [ENSG00000244331.1]
WARNING, no entry stored in dbm for [ENSG00000257261.6]
WARNING, no entry stored in dbm for [ENSG00000262202.4]
WARNING, no entry stored in dbm for [ENSG00000250770.3]
WARNING, no entry stored in dbm for [ENSG00000254610.3]
WARNING, no entry stored in dbm for [ENSG00000248618.1]
* STAR-Fusion complete. See output: /tmp/nxf.s3HI74ZYeN/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)