Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/8598a0399a2abe993334a5a089d622/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.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/f6/d4f16c4f548a84fbbbf08b3e389138/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/d4f16c4f548a84fbbbf08b3e389138/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/06f8ed66b1cb4915c27073fc207633/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/06f8ed66b1cb4915c27073fc207633/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.JI1ALB4lq6/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary
-sample contains 43072207 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir -J /tmp/nxf.JI1ALB4lq6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.Chimeric.out.junction -O /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.JI1ALB4lq6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.Chimeric.out.junction
-building interval tree based on /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=100000.00/min
[20000], rate=120000.00/min
[30000], rate=150000.00/min
[40000], rate=171428.57/min
[50000], rate=187500.00/min
[60000], rate=189473.68/min
[70000], rate=190909.09/min
[80000], rate=200000.00/min
[90000], rate=192857.14/min
[100000], rate=171428.57/min
[110000], rate=143478.26/min
[120000], rate=130909.09/min
[130000], rate=120000.00/min
[140000], rate=116666.67/min
[150000], rate=115384.62/min
[160000], rate=109090.91/min
[170000], rate=99029.13/min
[180000], rate=90000.00/min
[190000], rate=85714.29/min
[200000], rate=82191.78/min
[210000], rate=80769.23/min
[220000], rate=80981.60/min
[230000], rate=80701.75/min
[240000], rate=80898.88/min
[250000], rate=80213.90/min
[260000], rate=76847.29/min
[270000], rate=75000.00/min
[280000], rate=73043.48/min
[290000], rate=71900.83/min
[300000], rate=70312.50/min
[310000], rate=69144.98/min
[320000], rate=68817.20/min
[330000], rate=68750.00/min
[340000], rate=69152.54/min
[350000], rate=68403.91/min
[360000], rate=67080.75/min
[370000], rate=66268.66/min
[380000], rate=65706.05/min
[390000], rate=65363.13/min
[400000], rate=65217.39/min
[410000], rate=64907.65/min
[420000], rate=65116.28/min
[430000], rate=65316.46/min
[440000], rate=65508.68/min
[450000], rate=66014.67/min
[460000], rate=65558.19/min
[470000], rate=65127.02/min
[480000], rate=65011.29/min
[490000], rate=65044.25/min
[500000], rate=65217.39/min
[510000], rate=65948.28/min
[520000], rate=65684.21/min
[530000], rate=65297.74/min
[540000], rate=65191.15/min
[550000], rate=65088.76/min
[560000], rate=65242.72/min
[570000], rate=65391.97/min
[580000], rate=65784.50/min
[590000], rate=65434.38/min
[600000], rate=65335.75/min
[610000], rate=65357.14/min
[620000], rate=65492.96/min
[630000], rate=65625.00/min -building interval tree based on /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=46153.85/min
[20000], rate=46153.85/min
[30000], rate=43902.44/min
[40000], rate=44444.44/min
[50000], rate=44117.65/min
[60000], rate=44444.44/min
[70000], rate=43750.00/min
[80000], rate=43636.36/min
[90000], rate=43200.00/min
[100000], rate=42857.14/min
[110000], rate=42857.14/min
[120000], rate=42352.94/min
[130000], rate=41935.48/min
[140000], rate=41791.04/min
[150000], rate=41860.47/min
[160000], rate=42105.26/min
[170000], rate=42500.00/min
[180000], rate=43200.00/min
[190000], rate=44186.05/min
[200000], rate=44280.44/min
[210000], rate=43750.00/min
[220000], rate=43137.25/min
[230000], rate=43125.00/min
[240000], rate=43243.24/min
[250000], rate=43227.67/min
[260000], rate=43575.42/min
[270000], rate=43902.44/min
[280000], rate=44327.18/min
[290000], rate=44961.24/min
[300000], rate=45685.28/min
[310000], rate=46153.85/min
[320000], rate=46715.33/min
[330000], rate=47368.42/min
[340000], rate=47552.45/min
[350000], rate=47727.27/min
[360000], rate=47893.57/min
[370000], rate=48366.01/min
[380000], rate=49032.26/min
[390000], rate=49893.39/min
[400000], rate=50739.96/min
[410000], rate=51572.33/min
[420000], rate=52282.16/min
[430000], rate=53526.97/min
[440000], rate=54432.99/min
[450000], rate=55214.72/min
[460000], rate=56097.56/min
[470000], rate=56400.00/min
[480000], rate=56250.00/min
[490000], rate=56106.87/min
[500000], rate=56179.78/min
[510000], rate=56353.59/min
[520000], rate=56624.32/min
[530000], rate=57091.56/min
[540000], rate=56742.56/min
[550000], rate=56506.85/min
[560000], rate=56470.59/min
[570000], rate=56342.67/min
[580000], rate=56401.94/min
[590000], rate=56459.33/min
[600000], rate=56514.91/min
[610000], rate=56568.78/min
[620000], rate=56621.00/min
[630000], rate=56756.76/min -building interval tree based on /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=42857.14/min
[20000], rate=44444.44/min
[30000], rate=45000.00/min
[40000], rate=44444.44/min
[50000], rate=44776.12/min
[60000], rate=45000.00/min
[70000], rate=46153.85/min
[80000], rate=47524.75/min
[90000], rate=48214.29/min
[100000], rate=48780.49/min
[110000], rate=49624.06/min
[120000], rate=49655.17/min
[130000], rate=50649.35/min
[140000], rate=52173.91/min
[150000], rate=53571.43/min
[160000], rate=53932.58/min
[170000], rate=55135.14/min
[180000], rate=54271.36/min
[190000], rate=52777.78/min
[200000], rate=51282.05/min
[210000], rate=50602.41/min
[220000], rate=50381.68/min
[230000], rate=50364.96/min
[240000], rate=50704.23/min
[250000], rate=51194.54/min
[260000], rate=52000.00/min
[270000], rate=52768.73/min
[280000], rate=51692.31/min
[290000], rate=50728.86/min
[300000], rate=49861.50/min
[310000], rate=49076.52/min
[320000], rate=48730.96/min
[330000], rate=48648.65/min
[340000], rate=48226.95/min
[350000], rate=48275.86/min
[360000], rate=48214.29/min
[370000], rate=48260.87/min
[380000], rate=48305.08/min
[390000], rate=48447.20/min
[400000], rate=48780.49/min
[410000], rate=49298.60/min
[420000], rate=49704.14/min
[430000], rate=50292.40/min
[440000], rate=50574.71/min
[450000], rate=50847.46/min
[460000], rate=51301.12/min
[470000], rate=51838.24/min
[480000], rate=52173.91/min
[490000], rate=52593.92/min
[500000], rate=53003.53/min
[510000], rate=53310.10/min
[520000], rate=53700.52/min
[530000], rate=54173.76/min
[540000], rate=54453.78/min
[550000], rate=54817.28/min
[560000], rate=55172.41/min
[570000], rate=55339.81/min
[580000], rate=54889.59/min
[590000], rate=54629.63/min
[600000], rate=54380.66/min
[610000], rate=54302.67/min
[620000], rate=54306.57/min
[630000], rate=54310.34/min -building interval tree based on /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=120000.00/min
[20000], rate=120000.00/min
[30000], rate=105882.35/min
[40000], rate=92307.69/min
[50000], rate=66666.67/min
[60000], rate=57142.86/min
[70000], rate=50602.41/min
[80000], rate=46153.85/min
[90000], rate=44262.30/min
[100000], rate=43478.26/min
[110000], rate=42857.14/min
[120000], rate=42857.14/min
[130000], rate=43093.92/min
[140000], rate=43076.92/min
[150000], rate=43269.23/min
[160000], rate=43438.91/min
[170000], rate=43965.52/min
[180000], rate=44444.44/min
[190000], rate=44881.89/min
[200000], rate=45801.53/min
[210000], rate=46840.15/min
[220000], rate=46975.09/min
[230000], rate=47260.27/min
[240000], rate=47682.12/min
[250000], rate=48076.92/min
[260000], rate=48598.13/min
[270000], rate=49240.12/min
[280000], rate=50000.00/min
[290000], rate=50000.00/min
[300000], rate=49586.78/min
[310000], rate=49206.35/min
[320000], rate=48979.59/min
[330000], rate=48648.65/min
[340000], rate=48456.06/min
[350000], rate=48275.86/min
[360000], rate=48000.00/min
[370000], rate=47844.83/min
[380000], rate=47500.00/min
[390000], rate=47177.42/min
[400000], rate=46966.73/min
[410000], rate=46768.06/min
[420000], rate=46494.46/min
[430000], rate=46319.57/min
[440000], rate=46234.68/min
[450000], rate=45996.59/min
[460000], rate=45771.14/min
[470000], rate=45557.35/min
[480000], rate=45425.87/min
[490000], rate=45300.46/min
[500000], rate=45180.72/min
[510000], rate=45066.27/min
[520000], rate=45021.65/min
[530000], rate=44978.78/min
[540000], rate=44813.28/min
[550000], rate=44715.45/min
[560000], rate=44621.51/min
[570000], rate=44589.31/min
[580000], rate=44501.28/min
[590000], rate=44472.36/min
[600000], rate=44389.64/min
[610000], rate=44363.64/min
[620000], rate=44285.71/min
[630000], rate=44158.88/min
[640000], rate=44137.93/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir --filt_file /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
2857142.86 reads per min processed...
2869565.22 reads per min processed...
2880000.00 reads per min processed...
2888888.89 reads per min processed...
2896551.72 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3000000.00 reads per min processed...
3076923.08 reads per min processed...
3073170.73 reads per min processed...
3069767.44 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.JI1ALB4lq6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.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.JI1ALB4lq6/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -46205.261238
EM: Round [1] log likelihood: -46165.527403
EM: Round [2] log likelihood: -46151.394785
EM: Round [3] log likelihood: -46144.745671
EM: Round [4] log likelihood: -46141.276453
EM: Round [5] log likelihood: -46139.389752
EM: Round [6] log likelihood: -46138.336728
EM: Round [7] log likelihood: -46137.733567
EM: Round [8] log likelihood: -46137.377846
EM: Round [9] log likelihood: -46137.161247
EM: Round [10] log likelihood: -46137.024891
EM: Round [11] log likelihood: -46136.936129
EM: Round [12] log likelihood: -46136.876434
EM: Round [13] log likelihood: -46136.835018
EM: Round [14] log likelihood: -46136.805433
EM: Round [15] log likelihood: -46136.783717
EM: Round [16] log likelihood: -46136.767376
EM: Round [17] log likelihood: -46136.754794
EM: Round [18] log likelihood: -46136.744904
EM: Round [19] log likelihood: -46136.736984
EM: Round [20] log likelihood: -46136.730533
EM: Round [21] log likelihood: -46136.725200
EM: Round [22] log likelihood: -46136.720731
EM: Round [23] log likelihood: -46136.716943
EM: Round [24] log likelihood: -46136.713696
EM: Round [25] log likelihood: -46136.710889
EM: Round [26] log likelihood: -46136.708440
EM: Round [27] log likelihood: -46136.706289
EM: Round [28] log likelihood: -46136.704386
EM: Round [29] log likelihood: -46136.702693
EM: Round [30] log likelihood: -46136.701177
EM: Round [31] log likelihood: -46136.699814
EM: Round [32] log likelihood: -46136.698583
EM: Round [33] log likelihood: -46136.697466
EM: Round [34] log likelihood: -46136.696448
EM: Round [35] log likelihood: -46136.695517
EM: Round [36] log likelihood: -46136.694664
EM: Round [37] log likelihood: -46136.693878
EM: Round [38] log likelihood: -46136.693154
EM: Round [39] log likelihood: -46136.692483
EM: Round [40] log likelihood: -46136.691862
EM: Round [41] log likelihood: -46136.691284
EM: Round [42] log likelihood: -46136.690746
EM: Round [43] log likelihood: -46136.690244
EM: Round [44] log likelihood: -46136.689775
EM: Round [45] log likelihood: -46136.689335
EM: Round [46] log likelihood: -46136.688924
EM: Round [47] log likelihood: -46136.688537
EM: Round [48] log likelihood: -46136.688174
EM: Round [49] log likelihood: -46136.687833
EM: Round [50] log likelihood: -46136.687512
EM: Round [51] log likelihood: -46136.687209
EM: Round [52] log likelihood: -46136.686923
EM: Round [53] log likelihood: -46136.686654
EM: Round [54] log likelihood: -46136.686400
EM: Round [55] log likelihood: -46136.686160
EM: Round [56] log likelihood: -46136.685933
EM: Round [57] log likelihood: -46136.685718
EM: Round [58] log likelihood: -46136.685515
EM: Round [59] log likelihood: -46136.685323
EM: Round [60] log likelihood: -46136.685141
EM: Round [61] log likelihood: -46136.684969
EM: Round [62] log likelihood: -46136.684807
EM: Round [63] log likelihood: -46136.684652
EM: Round [64] log likelihood: -46136.684507
EM: Round [65] log likelihood: -46136.684368
EM: Round [66] log likelihood: -46136.684237
EM: Round [67] log likelihood: -46136.684113
EM: Round [68] log likelihood: -46136.683996
EM: Round [69] log likelihood: -46136.683884
EM: Round [70] log likelihood: -46136.683779
EM: Round [71] log likelihood: -46136.683678
EM: Round [72] log likelihood: -46136.683584
EM: Stopping iterations at round 72 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -46132.549660
EM: Round [1] log likelihood: -46106.265534
EM: Round [2] log likelihood: -46097.309508
EM: Round [3] log likelihood: -46093.188958
EM: Round [4] log likelihood: -46091.085246
EM: Round [5] log likelihood: -46089.971694
EM: Round [6] log likelihood: -46089.371967
EM: Round [7] log likelihood: -46089.043742
EM: Round [8] log likelihood: -46088.860605
EM: Round [9] log likelihood: -46088.756091
EM: Round [10] log likelihood: -46088.694956
EM: Round [11] log likelihood: -46088.658273
EM: Round [12] log likelihood: -46088.635700
EM: Round [13] log likelihood: -46088.621471
EM: Round [14] log likelihood: -46088.612299
EM: Round [15] log likelihood: -46088.606264
EM: Round [16] log likelihood: -46088.602219
EM: Round [17] log likelihood: -46088.599462
EM: Round [18] log likelihood: -46088.597555
EM: Round [19] log likelihood: -46088.596217
EM: Round [20] log likelihood: -46088.595267
EM: Round [21] log likelihood: -46088.594584
EM: Round [22] log likelihood: -46088.594089
EM: Round [23] log likelihood: -46088.593725
EM: Round [24] log likelihood: -46088.593457
EM: Round [25] log likelihood: -46088.593256
EM: Round [26] log likelihood: -46088.593105
EM: Round [27] log likelihood: -46088.592991
EM: Round [28] log likelihood: -46088.592904
EM: Stopping iterations at round 28 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.JI1ALB4lq6/./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.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.JI1ALB4lq6/./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.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 43072207 > /tmp/nxf.JI1ALB4lq6/./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.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir > /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir --annotate /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.JI1ALB4lq6/./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.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir
-done, see /tmp/nxf.JI1ALB4lq6/./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.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.JI1ALB4lq6/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 405, filtered: 3862)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.JI1ALB4lq6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.JI1ALB4lq6/./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.JI1ALB4lq6/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 [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000235749.3]
WARNING, no entry stored in dbm for [ENSG00000234420.7]
WARNING, no entry stored in dbm for [ENSG00000254170.1]
WARNING, no entry stored in dbm for [ENSG00000236830.7]
WARNING, no entry stored in dbm for [ENSG00000286780.1]
WARNING, no entry stored in dbm for [ENSG00000259848.9]
WARNING, no entry stored in dbm for [ENSG00000225400.1]
WARNING, no entry stored in dbm for [ENSG00000285533.2]
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 [ENSG00000214559.3]
WARNING, no entry stored in dbm for [ENSG00000271237.1]
WARNING, no entry stored in dbm for [ENSG00000128438.10]
WARNING, no entry stored in dbm for [ENSG00000206623.1]
WARNING, no entry stored in dbm for [ENSG00000200224.2]
WARNING, no entry stored in dbm for [ENSG00000252628.2]
WARNING, no entry stored in dbm for [ENSG00000207204.1]
WARNING, no entry stored in dbm for [ENSG00000202350.1]
WARNING, no entry stored in dbm for [ENSG00000202082.2]
WARNING, no entry stored in dbm for [ENSG00000202296.1]
WARNING, no entry stored in dbm for [ENSG00000206896.1]
WARNING, no entry stored in dbm for [ENSG00000260630.7]
WARNING, no entry stored in dbm for [ENSG00000285051.2]
WARNING, no entry stored in dbm for [ENSG00000224081.9]
WARNING, no entry stored in dbm for [ENSG00000226448.1]
WARNING, no entry stored in dbm for [ENSG00000242071.3]
WARNING, no entry stored in dbm for [ENSG00000241157.1]
WARNING, no entry stored in dbm for [ENSG00000270723.1]
WARNING, no entry stored in dbm for [ENSG00000223508.5]
WARNING, no entry stored in dbm for [ENSG00000212939.2]
WARNING, no entry stored in dbm for [ENSG00000224079.1]
WARNING, no entry stored in dbm for [ENSG00000207789.1]
WARNING, no entry stored in dbm for [ENSG00000199075.1]
WARNING, no entry stored in dbm for [ENSG00000249162.1]
WARNING, no entry stored in dbm for [ENSG00000218052.5]
WARNING, no entry stored in dbm for [ENSG00000244479.7]
WARNING, no entry stored in dbm for [ENSG00000228960.6]
WARNING, no entry stored in dbm for [ENSG00000223482.8]
WARNING, no entry stored in dbm for [ENSG00000255213.1]
WARNING, no entry stored in dbm for [ENSG00000255213.1]
WARNING, no entry stored in dbm for [ENSG00000267607.1]
WARNING, no entry stored in dbm for [ENSG00000259374.2]
WARNING, no entry stored in dbm for [ENSG00000283972.1]
WARNING, no entry stored in dbm for [ENSG00000198496.12]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000201793.1]
WARNING, no entry stored in dbm for [ENSG00000202058.1]
WARNING, no entry stored in dbm for [ENSG00000271394.1]
WARNING, no entry stored in dbm for [ENSG00000277888.1]
WARNING, no entry stored in dbm for [ENSG00000257859.2]
WARNING, no entry stored in dbm for [ENSG00000214070.3]
WARNING, no entry stored in dbm for [ENSG00000238045.9]
WARNING, no entry stored in dbm for [ENSG00000232517.2]
WARNING, no entry stored in dbm for [ENSG00000228730.2]
WARNING, no entry stored in dbm for [ENSG00000248727.6]
WARNING, no entry stored in dbm for [ENSG00000232650.6]
WARNING, no entry stored in dbm for [ENSG00000228666.1]
WARNING, no entry stored in dbm for [ENSG00000286675.1]
WARNING, no entry stored in dbm for [ENSG00000214708.4]
WARNING, no entry stored in dbm for [ENSG00000253774.1]
WARNING, no entry stored in dbm for [ENSG00000204625.10]
WARNING, no entry stored in dbm for [ENSG00000233299.1]
WARNING, no entry stored in dbm for [ENSG00000218261.1]
WARNING, no entry stored in dbm for [ENSG00000214433.4]
WARNING, no entry stored in dbm for [ENSG00000239533.6]
WARNING, no entry stored in dbm for [ENSG00000244056.3]
WARNING, no entry stored in dbm for [ENSG00000235269.2]
WARNING, no entry stored in dbm for [ENSG00000234338.1]
WARNING, no entry stored in dbm for [ENSG00000249072.1]
WARNING, no entry stored in dbm for [ENSG00000228928.1]
WARNING, no entry stored in dbm for [ENSG00000244383.2]
WARNING, no entry stored in dbm for [ENSG00000174407.13]
WARNING, no entry stored in dbm for [ENSG00000222047.9]
WARNING, no entry stored in dbm for [ENSG00000216859.1]
WARNING, no entry stored in dbm for [ENSG00000204338.8]
WARNING, no entry stored in dbm for [ENSG00000284471.1]
WARNING, no entry stored in dbm for [ENSG00000212978.6]
WARNING, no entry stored in dbm for [ENSG00000241104.5]
WARNING, no entry stored in dbm for [ENSG00000240498.9]
WARNING, no entry stored in dbm for [ENSG00000227835.8]
WARNING, no entry stored in dbm for [ENSG00000205930.10]
WARNING, no entry stored in dbm for [ENSG00000259259.1]
WARNING, no entry stored in dbm for [ENSG00000277739.1]
WARNING, no entry stored in dbm for [ENSG00000283568.1]
WARNING, no entry stored in dbm for [ENSG00000287028.1]
WARNING, no entry stored in dbm for [ENSG00000222012.1]
WARNING, no entry stored in dbm for [ENSG00000203987.3]
WARNING, no entry stored in dbm for [ENSG00000217557.1]
WARNING, no entry stored in dbm for [ENSG00000223676.1]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000286652.1]
WARNING, no entry stored in dbm for [ENSG00000254612.2]
WARNING, no entry stored in dbm for [ENSG00000234325.1]
WARNING, no entry stored in dbm for [ENSG00000249162.1]
WARNING, no entry stored in dbm for [ENSG00000227264.3]
WARNING, no entry stored in dbm for [ENSG00000285062.1]
WARNING, no entry stored in dbm for [ENSG00000275140.1]
WARNING, no entry stored in dbm for [ENSG00000278791.1]
WARNING, no entry stored in dbm for [ENSG00000250405.2]
WARNING, no entry stored in dbm for [ENSG00000248376.2]
WARNING, no entry stored in dbm for [ENSG00000205890.3]
WARNING, no entry stored in dbm for [ENSG00000214182.5]
WARNING, no entry stored in dbm for [ENSG00000223373.1]
WARNING, no entry stored in dbm for [ENSG00000245025.3]
WARNING, no entry stored in dbm for [ENSG00000250159.7]
WARNING, no entry stored in dbm for [ENSG00000241462.1]
WARNING, no entry stored in dbm for [ENSG00000227615.1]
WARNING, no entry stored in dbm for [ENSG00000287129.1]
WARNING, no entry stored in dbm for [ENSG00000231646.6]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000239268.3]
WARNING, no entry stored in dbm for [ENSG00000273084.1]
WARNING, no entry stored in dbm for [ENSG00000259418.1]
WARNING, no entry stored in dbm for [ENSG00000240687.2]
WARNING, no entry stored in dbm for [ENSG00000253361.3]
WARNING, no entry stored in dbm for [ENSG00000285712.1]
WARNING, no entry stored in dbm for [ENSG00000226535.1]
WARNING, no entry stored in dbm for [ENSG00000254859.1]
WARNING, no entry stored in dbm for [ENSG00000279738.1]
WARNING, no entry stored in dbm for [ENSG00000229334.1]
WARNING, no entry stored in dbm for [ENSG00000185641.6]
WARNING, no entry stored in dbm for [ENSG00000206567.10]
WARNING, no entry stored in dbm for [ENSG00000259407.1]
WARNING, no entry stored in dbm for [ENSG00000240827.1]
WARNING, no entry stored in dbm for [ENSG00000230508.1]
WARNING, no entry stored in dbm for [ENSG00000279569.1]
WARNING, no entry stored in dbm for [ENSG00000234929.2]
WARNING, no entry stored in dbm for [ENSG00000249839.1]
WARNING, no entry stored in dbm for [ENSG00000288585.1]
WARNING, no entry stored in dbm for [ENSG00000272372.1]
WARNING, no entry stored in dbm for [ENSG00000269604.1]
* STAR-Fusion complete. See output: /tmp/nxf.JI1ALB4lq6/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)