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/62/6536c8bb6092baf57c0e0fefb78c08/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/d0c178e6613c97a728faea8a172cde/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/d0c178e6613c97a728faea8a172cde/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/6536c8bb6092baf57c0e0fefb78c08/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/99c40323c241ef8c796831fa72cffc/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.a6P2jx5TIm/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary
-sample contains 9022667 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir -J /tmp/nxf.a6P2jx5TIm/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction -O /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.a6P2jx5TIm/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction
-building interval tree based on /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=54545.45/min
[20000], rate=54545.45/min
[30000], rate=64285.71/min
[40000], rate=60000.00/min
[50000], rate=58823.53/min
[60000], rate=54545.45/min
[70000], rate=53164.56/min
[80000], rate=53932.58/min
[90000], rate=52941.18/min
[100000], rate=53571.43/min
[110000], rate=52800.00/min
[120000], rate=53333.33/min
[130000], rate=53424.66/min
[140000], rate=53503.18/min
[150000], rate=46875.00/min
[160000], rate=44239.63/min
[170000], rate=43589.74/min
[180000], rate=43200.00/min
[190000], rate=42696.63/min
[200000], rate=42105.26/min
[210000], rate=42000.00/min
[220000], rate=40615.38/min
[230000], rate=40350.88/min
[240000], rate=40223.46/min -building interval tree based on /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=37500.00/min
[20000], rate=48000.00/min
[30000], rate=46153.85/min
[40000], rate=40000.00/min
[50000], rate=36144.58/min
[60000], rate=36363.64/min
[70000], rate=37168.14/min
[80000], rate=37500.00/min
[90000], rate=37500.00/min
[100000], rate=38461.54/min
[110000], rate=38150.29/min
[120000], rate=38095.24/min
[130000], rate=38235.29/min
[140000], rate=38356.16/min
[150000], rate=38461.54/min
[160000], rate=37795.28/min
[170000], rate=37500.00/min
[180000], rate=37370.24/min
[190000], rate=36893.20/min
[200000], rate=36923.08/min
[210000], rate=37724.55/min
[220000], rate=37288.14/min
[230000], rate=37500.00/min
[240000], rate=38196.29/min -building interval tree based on /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=75000.00/min
[20000], rate=70588.24/min
[30000], rate=60000.00/min
[40000], rate=61538.46/min
[50000], rate=53571.43/min
[60000], rate=55384.62/min
[70000], rate=50602.41/min
[80000], rate=45714.29/min
[90000], rate=44262.30/min
[100000], rate=45112.78/min
[110000], rate=45205.48/min
[120000], rate=42105.26/min
[130000], rate=38235.29/min
[140000], rate=36521.74/min
[150000], rate=36290.32/min
[160000], rate=37209.30/min
[170000], rate=34576.27/min
[180000], rate=33230.77/min
[190000], rate=32664.76/min
[200000], rate=31830.24/min
[210000], rate=30215.83/min
[220000], rate=30626.45/min
[230000], rate=31011.24/min
[240000], rate=31236.44/min -building interval tree based on /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=75000.00/min
[20000], rate=70588.24/min
[30000], rate=72000.00/min
[40000], rate=68571.43/min
[50000], rate=71428.57/min
[60000], rate=70588.24/min
[70000], rate=72413.79/min
[80000], rate=68571.43/min
[90000], rate=65853.66/min
[100000], rate=54545.45/min
[110000], rate=42038.22/min
[120000], rate=34782.61/min
[130000], rate=32098.77/min
[140000], rate=31111.11/min
[150000], rate=31578.95/min
[160000], rate=31270.36/min
[170000], rate=31578.95/min
[180000], rate=31671.55/min
[190000], rate=30978.26/min
[200000], rate=30000.00/min
[210000], rate=29439.25/min
[220000], rate=29729.73/min
[230000], rate=29550.32/min
[240000], rate=29090.91/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir --filt_file /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
0.00 reads per min processed...
6000000.00 reads per min processed...
3600000.00 reads per min processed...
4000000.00 reads per min processed...
4285714.29 reads per min processed...
4500000.00 reads per min processed...
4200000.00 reads per min processed...
4000000.00 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.a6P2jx5TIm/BreastNP_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.a6P2jx5TIm/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -13888.687828
EM: Round [1] log likelihood: -13847.920813
EM: Round [2] log likelihood: -13830.027583
EM: Round [3] log likelihood: -13820.846434
EM: Round [4] log likelihood: -13815.834995
EM: Round [5] log likelihood: -13813.000028
EM: Round [6] log likelihood: -13811.339629
EM: Round [7] log likelihood: -13810.327730
EM: Round [8] log likelihood: -13809.684293
EM: Round [9] log likelihood: -13809.257820
EM: Round [10] log likelihood: -13808.964199
EM: Round [11] log likelihood: -13808.755167
EM: Round [12] log likelihood: -13808.602031
EM: Round [13] log likelihood: -13808.487110
EM: Round [14] log likelihood: -13808.399125
EM: Round [15] log likelihood: -13808.330640
EM: Round [16] log likelihood: -13808.276599
EM: Round [17] log likelihood: -13808.233469
EM: Round [18] log likelihood: -13808.198716
EM: Round [19] log likelihood: -13808.170487
EM: Round [20] log likelihood: -13808.147398
EM: Round [21] log likelihood: -13808.128402
EM: Round [22] log likelihood: -13808.112693
EM: Round [23] log likelihood: -13808.099642
EM: Round [24] log likelihood: -13808.088757
EM: Round [25] log likelihood: -13808.079647
EM: Round [26] log likelihood: -13808.071997
EM: Round [27] log likelihood: -13808.065556
EM: Round [28] log likelihood: -13808.060118
EM: Round [29] log likelihood: -13808.055516
EM: Round [30] log likelihood: -13808.051614
EM: Round [31] log likelihood: -13808.048298
EM: Round [32] log likelihood: -13808.045474
EM: Round [33] log likelihood: -13808.043066
EM: Round [34] log likelihood: -13808.041009
EM: Round [35] log likelihood: -13808.039249
EM: Round [36] log likelihood: -13808.037740
EM: Round [37] log likelihood: -13808.036445
EM: Round [38] log likelihood: -13808.035331
EM: Round [39] log likelihood: -13808.034373
EM: Round [40] log likelihood: -13808.033547
EM: Round [41] log likelihood: -13808.032834
EM: Round [42] log likelihood: -13808.032217
EM: Round [43] log likelihood: -13808.031683
EM: Round [44] log likelihood: -13808.031221
EM: Round [45] log likelihood: -13808.030819
EM: Round [46] log likelihood: -13808.030470
EM: Round [47] log likelihood: -13808.030166
EM: Round [48] log likelihood: -13808.029901
EM: Round [49] log likelihood: -13808.029670
EM: Round [50] log likelihood: -13808.029468
EM: Round [51] log likelihood: -13808.029291
EM: Round [52] log likelihood: -13808.029136
EM: Round [53] log likelihood: -13808.029000
EM: Round [54] log likelihood: -13808.028880
EM: Round [55] log likelihood: -13808.028774
EM: Round [56] log likelihood: -13808.028681
EM: Stopping iterations at round 56 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -13879.529658
EM: Round [1] log likelihood: -13842.984914
EM: Round [2] log likelihood: -13827.261309
EM: Round [3] log likelihood: -13819.261221
EM: Round [4] log likelihood: -13814.902222
EM: Round [5] log likelihood: -13812.433585
EM: Round [6] log likelihood: -13810.983285
EM: Round [7] log likelihood: -13810.095432
EM: Round [8] log likelihood: -13809.527774
EM: Round [9] log likelihood: -13809.149211
EM: Round [10] log likelihood: -13808.886854
EM: Round [11] log likelihood: -13808.698815
EM: Round [12] log likelihood: -13808.560140
EM: Round [13] log likelihood: -13808.455413
EM: Round [14] log likelihood: -13808.374764
EM: Round [15] log likelihood: -13808.311654
EM: Round [16] log likelihood: -13808.261614
EM: Round [17] log likelihood: -13808.221503
EM: Round [18] log likelihood: -13808.189057
EM: Round [19] log likelihood: -13808.162611
EM: Round [20] log likelihood: -13808.140914
EM: Round [21] log likelihood: -13808.123014
EM: Round [22] log likelihood: -13808.108177
EM: Round [23] log likelihood: -13808.095826
EM: Round [24] log likelihood: -13808.085508
EM: Round [25] log likelihood: -13808.076860
EM: Round [26] log likelihood: -13808.069592
EM: Round [27] log likelihood: -13808.063467
EM: Round [28] log likelihood: -13808.058294
EM: Round [29] log likelihood: -13808.053915
EM: Round [30] log likelihood: -13808.050202
EM: Round [31] log likelihood: -13808.047048
EM: Round [32] log likelihood: -13808.044364
EM: Round [33] log likelihood: -13808.042077
EM: Round [34] log likelihood: -13808.040125
EM: Round [35] log likelihood: -13808.038457
EM: Round [36] log likelihood: -13808.037029
EM: Round [37] log likelihood: -13808.035806
EM: Round [38] log likelihood: -13808.034756
EM: Round [39] log likelihood: -13808.033854
EM: Round [40] log likelihood: -13808.033079
EM: Round [41] log likelihood: -13808.032411
EM: Round [42] log likelihood: -13808.031835
EM: Round [43] log likelihood: -13808.031338
EM: Round [44] log likelihood: -13808.030908
EM: Round [45] log likelihood: -13808.030536
EM: Round [46] log likelihood: -13808.030213
EM: Round [47] log likelihood: -13808.029934
EM: Round [48] log likelihood: -13808.029691
EM: Round [49] log likelihood: -13808.029479
EM: Round [50] log likelihood: -13808.029295
EM: Round [51] log likelihood: -13808.029134
EM: Round [52] log likelihood: -13808.028994
EM: Round [53] log likelihood: -13808.028871
EM: Round [54] log likelihood: -13808.028764
EM: Round [55] log likelihood: -13808.028669
EM: Stopping iterations at round 55 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9022667 > /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir > /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir --annotate /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir
-done, see /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 82, filtered: 1386)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000260231.2]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000229807.12]
WARNING, no entry stored in dbm for [ENSG00000259021.2]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000274727.1]
WARNING, no entry stored in dbm for [ENSG00000266088.6]
WARNING, no entry stored in dbm for [ENSG00000241081.1]
WARNING, no entry stored in dbm for [ENSG00000225483.1]
WARNING, no entry stored in dbm for [ENSG00000203993.6]
WARNING, no entry stored in dbm for [ENSG00000181577.16]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000231437.3]
WARNING, no entry stored in dbm for [ENSG00000239921.6]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000239921.6]
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 [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGL.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 [ENSG00000281383.1]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000280800.1]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000281181.1]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000280614.1]
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 [ENSG00000214548.18]
WARNING, no entry stored in dbm for [ENSG00000279141.3]
WARNING, no entry stored in dbm for [ENSG00000236333.4]
WARNING, no entry stored in dbm for [ENSG00000234975.6]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000259098.1]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000259098.1]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000279694.1]
WARNING, no entry stored in dbm for [ENSG00000286335.1]
WARNING, no entry stored in dbm for [ENSG00000243224.1]
* STAR-Fusion complete. See output: /tmp/nxf.a6P2jx5TIm/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)