.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/e50ceef7ed8a9ec1ebc85b4ac13ef9/.command.log
Size: 26.8 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/bd23407f957e59aae9828da014a54f/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
  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/ec/e50ceef7ed8a9ec1ebc85b4ac13ef9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/e50ceef7ed8a9ec1ebc85b4ac13ef9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/4de7802266e95e36763fef62c5e2d8/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/bd23407f957e59aae9828da014a54f/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.bowiNehLnx/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.bowiNehLnx/./star-fusion.preliminary
-sample contains 9095254 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir  -J /tmp/nxf.bowiNehLnx/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.bowiNehLnx/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[330000], rate=91666.67/min -building interval tree based on /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[340000], rate=91891.89/min -building interval tree based on /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[330000], rate=82157.68/min -building interval tree based on /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[330000], rate=71739.13/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.bowiNehLnx/./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...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 5000000.00 reads per min processed...  
 5142857.14 reads per min processed...  
 5250000.00 reads per min processed...  
 5333333.33 reads per min processed...  
 5400000.00 reads per min processed...  
 5000000.00 reads per min processed...  
 5076923.08 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.bowiNehLnx/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_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.bowiNehLnx/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -21728.243281
EM: Round [1] log likelihood: -21663.712832
EM: Round [2] log likelihood: -21636.257725
EM: Round [3] log likelihood: -21622.321145
EM: Round [4] log likelihood: -21614.647840
EM: Round [5] log likelihood: -21610.249488
EM: Round [6] log likelihood: -21607.649787
EM: Round [7] log likelihood: -21606.064707
EM: Round [8] log likelihood: -21605.067046
EM: Round [9] log likelihood: -21604.419437
EM: Round [10] log likelihood: -21603.986695
EM: Round [11] log likelihood: -21603.689623
EM: Round [12] log likelihood: -21603.480497
EM: Round [13] log likelihood: -21603.329785
EM: Round [14] log likelihood: -21603.218760
EM: Round [15] log likelihood: -21603.135273
EM: Round [16] log likelihood: -21603.071273
EM: Round [17] log likelihood: -21603.021314
EM: Round [18] log likelihood: -21602.981646
EM: Round [19] log likelihood: -21602.949642
EM: Round [20] log likelihood: -21602.923431
EM: Round [21] log likelihood: -21602.901659
EM: Round [22] log likelihood: -21602.883335
EM: Round [23] log likelihood: -21602.867726
EM: Round [24] log likelihood: -21602.854279
EM: Round [25] log likelihood: -21602.842574
EM: Round [26] log likelihood: -21602.832290
EM: Round [27] log likelihood: -21602.823177
EM: Round [28] log likelihood: -21602.815039
EM: Round [29] log likelihood: -21602.807721
EM: Round [30] log likelihood: -21602.801100
EM: Round [31] log likelihood: -21602.795077
EM: Round [32] log likelihood: -21602.789570
EM: Round [33] log likelihood: -21602.784513
EM: Round [34] log likelihood: -21602.779852
EM: Round [35] log likelihood: -21602.775540
EM: Round [36] log likelihood: -21602.771538
EM: Round [37] log likelihood: -21602.767815
EM: Round [38] log likelihood: -21602.764343
EM: Round [39] log likelihood: -21602.761097
EM: Round [40] log likelihood: -21602.758056
EM: Round [41] log likelihood: -21602.755204
EM: Round [42] log likelihood: -21602.752523
EM: Round [43] log likelihood: -21602.749999
EM: Round [44] log likelihood: -21602.747621
EM: Round [45] log likelihood: -21602.745377
EM: Round [46] log likelihood: -21602.743258
EM: Round [47] log likelihood: -21602.741253
EM: Round [48] log likelihood: -21602.739355
EM: Round [49] log likelihood: -21602.737556
EM: Round [50] log likelihood: -21602.735851
EM: Round [51] log likelihood: -21602.734232
EM: Round [52] log likelihood: -21602.732694
EM: Round [53] log likelihood: -21602.731232
EM: Round [54] log likelihood: -21602.729840
EM: Round [55] log likelihood: -21602.728516
EM: Round [56] log likelihood: -21602.727254
EM: Round [57] log likelihood: -21602.726050
EM: Round [58] log likelihood: -21602.724902
EM: Round [59] log likelihood: -21602.723806
EM: Round [60] log likelihood: -21602.722759
EM: Round [61] log likelihood: -21602.721759
EM: Round [62] log likelihood: -21602.720802
EM: Round [63] log likelihood: -21602.719886
EM: Round [64] log likelihood: -21602.719009
EM: Round [65] log likelihood: -21602.718170
EM: Round [66] log likelihood: -21602.717365
EM: Round [67] log likelihood: -21602.716593
EM: Round [68] log likelihood: -21602.715853
EM: Round [69] log likelihood: -21602.715143
EM: Round [70] log likelihood: -21602.714461
EM: Round [71] log likelihood: -21602.713805
EM: Round [72] log likelihood: -21602.713176
EM: Round [73] log likelihood: -21602.712570
EM: Round [74] log likelihood: -21602.711988
EM: Round [75] log likelihood: -21602.711428
EM: Round [76] log likelihood: -21602.710889
EM: Round [77] log likelihood: -21602.710370
EM: Round [78] log likelihood: -21602.709870
EM: Round [79] log likelihood: -21602.709389
EM: Round [80] log likelihood: -21602.708925
EM: Round [81] log likelihood: -21602.708478
EM: Round [82] log likelihood: -21602.708047
EM: Round [83] log likelihood: -21602.707631
EM: Round [84] log likelihood: -21602.707230
EM: Round [85] log likelihood: -21602.706843
EM: Round [86] log likelihood: -21602.706470
EM: Round [87] log likelihood: -21602.706109
EM: Round [88] log likelihood: -21602.705761
EM: Round [89] log likelihood: -21602.705425
EM: Round [90] log likelihood: -21602.705100
EM: Round [91] log likelihood: -21602.704787
EM: Round [92] log likelihood: -21602.704484
EM: Round [93] log likelihood: -21602.704191
EM: Round [94] log likelihood: -21602.703908
EM: Round [95] log likelihood: -21602.703634
EM: Round [96] log likelihood: -21602.703370
EM: Round [97] log likelihood: -21602.703114
EM: Round [98] log likelihood: -21602.702867
EM: Round [99] log likelihood: -21602.702628
EM: Round [100] log likelihood: -21602.702396
EM: Round [101] log likelihood: -21602.702173
EM: Round [102] log likelihood: -21602.701956
EM: Round [103] log likelihood: -21602.701747
EM: Round [104] log likelihood: -21602.701544
EM: Round [105] log likelihood: -21602.701348
EM: Round [106] log likelihood: -21602.701158
EM: Round [107] log likelihood: -21602.700974
EM: Round [108] log likelihood: -21602.700796
EM: Round [109] log likelihood: -21602.700624
EM: Round [110] log likelihood: -21602.700457
EM: Round [111] log likelihood: -21602.700296
EM: Round [112] log likelihood: -21602.700140
EM: Round [113] log likelihood: -21602.699988
EM: Round [114] log likelihood: -21602.699842
EM: Round [115] log likelihood: -21602.699700
EM: Round [116] log likelihood: -21602.699562
EM: Round [117] log likelihood: -21602.699429
EM: Round [118] log likelihood: -21602.699300
EM: Round [119] log likelihood: -21602.699175
EM: Round [120] log likelihood: -21602.699054
EM: Round [121] log likelihood: -21602.698936
EM: Round [122] log likelihood: -21602.698822
EM: Round [123] log likelihood: -21602.698712
EM: Round [124] log likelihood: -21602.698605
EM: Round [125] log likelihood: -21602.698502
EM: Round [126] log likelihood: -21602.698401
EM: Round [127] log likelihood: -21602.698304
EM: Stopping iterations at round 127 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -21708.793701
EM: Round [1] log likelihood: -21651.949833
EM: Round [2] log likelihood: -21629.000455
EM: Round [3] log likelihood: -21617.745881
EM: Round [4] log likelihood: -21611.692083
EM: Round [5] log likelihood: -21608.283091
EM: Round [6] log likelihood: -21606.299035
EM: Round [7] log likelihood: -21605.106278
EM: Round [8] log likelihood: -21604.365261
EM: Round [9] log likelihood: -21603.890054
EM: Round [10] log likelihood: -21603.576161
EM: Round [11] log likelihood: -21603.363085
EM: Round [12] log likelihood: -21603.214746
EM: Round [13] log likelihood: -21603.109028
EM: Round [14] log likelihood: -21603.032028
EM: Round [15] log likelihood: -21602.974795
EM: Round [16] log likelihood: -21602.931445
EM: Round [17] log likelihood: -21602.898025
EM: Round [18] log likelihood: -21602.871831
EM: Round [19] log likelihood: -21602.850980
EM: Round [20] log likelihood: -21602.834139
EM: Round [21] log likelihood: -21602.820348
EM: Round [22] log likelihood: -21602.808909
EM: Round [23] log likelihood: -21602.799306
EM: Round [24] log likelihood: -21602.791151
EM: Round [25] log likelihood: -21602.784153
EM: Round [26] log likelihood: -21602.778087
EM: Round [27] log likelihood: -21602.772781
EM: Round [28] log likelihood: -21602.768099
EM: Round [29] log likelihood: -21602.763935
EM: Round [30] log likelihood: -21602.760205
EM: Round [31] log likelihood: -21602.756840
EM: Round [32] log likelihood: -21602.753786
EM: Round [33] log likelihood: -21602.750998
EM: Round [34] log likelihood: -21602.748440
EM: Round [35] log likelihood: -21602.746082
EM: Round [36] log likelihood: -21602.743898
EM: Round [37] log likelihood: -21602.741867
EM: Round [38] log likelihood: -21602.739972
EM: Round [39] log likelihood: -21602.738199
EM: Round [40] log likelihood: -21602.736533
EM: Round [41] log likelihood: -21602.734965
EM: Round [42] log likelihood: -21602.733486
EM: Round [43] log likelihood: -21602.732086
EM: Round [44] log likelihood: -21602.730759
EM: Round [45] log likelihood: -21602.729499
EM: Round [46] log likelihood: -21602.728300
EM: Round [47] log likelihood: -21602.727158
EM: Round [48] log likelihood: -21602.726068
EM: Round [49] log likelihood: -21602.725027
EM: Round [50] log likelihood: -21602.724031
EM: Round [51] log likelihood: -21602.723077
EM: Round [52] log likelihood: -21602.722162
EM: Round [53] log likelihood: -21602.721284
EM: Round [54] log likelihood: -21602.720441
EM: Round [55] log likelihood: -21602.719631
EM: Round [56] log likelihood: -21602.718851
EM: Round [57] log likelihood: -21602.718101
EM: Round [58] log likelihood: -21602.717378
EM: Round [59] log likelihood: -21602.716681
EM: Round [60] log likelihood: -21602.716009
EM: Round [61] log likelihood: -21602.715361
EM: Round [62] log likelihood: -21602.714735
EM: Round [63] log likelihood: -21602.714130
EM: Round [64] log likelihood: -21602.713546
EM: Round [65] log likelihood: -21602.712981
EM: Round [66] log likelihood: -21602.712435
EM: Round [67] log likelihood: -21602.711906
EM: Round [68] log likelihood: -21602.711395
EM: Round [69] log likelihood: -21602.710900
EM: Round [70] log likelihood: -21602.710421
EM: Round [71] log likelihood: -21602.709957
EM: Round [72] log likelihood: -21602.709508
EM: Round [73] log likelihood: -21602.709072
EM: Round [74] log likelihood: -21602.708651
EM: Round [75] log likelihood: -21602.708242
EM: Round [76] log likelihood: -21602.707846
EM: Round [77] log likelihood: -21602.707461
EM: Round [78] log likelihood: -21602.707089
EM: Round [79] log likelihood: -21602.706728
EM: Round [80] log likelihood: -21602.706378
EM: Round [81] log likelihood: -21602.706038
EM: Round [82] log likelihood: -21602.705709
EM: Round [83] log likelihood: -21602.705390
EM: Round [84] log likelihood: -21602.705080
EM: Round [85] log likelihood: -21602.704779
EM: Round [86] log likelihood: -21602.704488
EM: Round [87] log likelihood: -21602.704205
EM: Round [88] log likelihood: -21602.703931
EM: Round [89] log likelihood: -21602.703664
EM: Round [90] log likelihood: -21602.703406
EM: Round [91] log likelihood: -21602.703156
EM: Round [92] log likelihood: -21602.702913
EM: Round [93] log likelihood: -21602.702677
EM: Round [94] log likelihood: -21602.702448
EM: Round [95] log likelihood: -21602.702226
EM: Round [96] log likelihood: -21602.702011
EM: Round [97] log likelihood: -21602.701802
EM: Round [98] log likelihood: -21602.701599
EM: Round [99] log likelihood: -21602.701403
EM: Round [100] log likelihood: -21602.701212
EM: Round [101] log likelihood: -21602.701027
EM: Round [102] log likelihood: -21602.700847
EM: Round [103] log likelihood: -21602.700673
EM: Round [104] log likelihood: -21602.700504
EM: Round [105] log likelihood: -21602.700340
EM: Round [106] log likelihood: -21602.700181
EM: Round [107] log likelihood: -21602.700027
EM: Round [108] log likelihood: -21602.699878
EM: Round [109] log likelihood: -21602.699733
EM: Round [110] log likelihood: -21602.699592
EM: Round [111] log likelihood: -21602.699455
EM: Round [112] log likelihood: -21602.699323
EM: Round [113] log likelihood: -21602.699194
EM: Round [114] log likelihood: -21602.699070
EM: Round [115] log likelihood: -21602.698949
EM: Round [116] log likelihood: -21602.698831
EM: Round [117] log likelihood: -21602.698718
EM: Round [118] log likelihood: -21602.698607
EM: Round [119] log likelihood: -21602.698500
EM: Round [120] log likelihood: -21602.698397
EM: Round [121] log likelihood: -21602.698296
EM: Round [122] log likelihood: -21602.698198
EM: Stopping iterations at round 122 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9095254 > /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir > /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir --annotate /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir
-done, see /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 101, filtered: 1571)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000234715.2]
WARNING, no entry stored in dbm for [ENSG00000267598.1]
WARNING, no entry stored in dbm for [ENSG00000229739.4]
WARNING, no entry stored in dbm for [ENSG00000251010.1]
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 [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000198555.7]
WARNING, no entry stored in dbm for [ENSG00000259945.1]
WARNING, no entry stored in dbm for [ENSG00000243352.3]
WARNING, no entry stored in dbm for [ENSG00000240116.3]
WARNING, no entry stored in dbm for [ENSG00000265735.2]
WARNING, no entry stored in dbm for [ENSG00000240116.3]
WARNING, no entry stored in dbm for [ENSG00000244230.3]
WARNING, no entry stored in dbm for [ENSG00000240116.3]
WARNING, no entry stored in dbm for [ENSG00000276168.1]
WARNING, no entry stored in dbm for [ENSG00000240116.3]
WARNING, no entry stored in dbm for [ENSG00000272068.1]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000287957.1]
WARNING, no entry stored in dbm for [ENSG00000231920.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000266053.2]
WARNING, no entry stored in dbm for [ENSG00000270799.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000267383.7]
WARNING, no entry stored in dbm for [ENSG00000286045.1]
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 [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000255182.2]
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 [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000181126.13]
WARNING, no entry stored in dbm for [ENSG00000227195.11]
WARNING, no entry stored in dbm for [ENSG00000270578.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000260464.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000263883.1]
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 [ENSG00000287449.1]
WARNING, no entry stored in dbm for [ENSG00000255306.1]
WARNING, no entry stored in dbm for [ENSG00000260879.1]
WARNING, no entry stored in dbm for [ENSG00000220685.3]
WARNING, no entry stored in dbm for [ENSG00000275613.2]
WARNING, no entry stored in dbm for [ENSG00000275340.1]
WARNING, no entry stored in dbm for [ENSG00000273230.1]
WARNING, no entry stored in dbm for [ENSG00000267169.2]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000264044.1]
WARNING, no entry stored in dbm for [ENSG00000277283.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.bowiNehLnx/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)