.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (OvarianNP_FFPE_L02_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/9218ab821a440e0b07e0759e935bdf/.command.err
Size: 22.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (OvarianNP_FFPE_L02_RNA_01_B23LG7FLT4_1)
Attempt
Content

-ctat genome lib [/tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.FDhZqGVzDG/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary
-sample contains 12183393 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir  -J /tmp/nxf.FDhZqGVzDG/OvarianNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.FDhZqGVzDG/OvarianNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=40000.00/min 
[20000], rate=44444.44/min 
[30000], rate=48648.65/min 
[40000], rate=53333.33/min 
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[60000], rate=58064.52/min 
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[100000], rate=73170.73/min 
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[300000], rate=102272.73/min 
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[380000], rate=88715.95/min 
[390000], rate=87640.45/min -building interval tree based on /tmp/nxf.FDhZqGVzDG/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=85714.29/min 
[30000], rate=94736.84/min 
[40000], rate=72727.27/min 
[50000], rate=68181.82/min 
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[100000], rate=73170.73/min 
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[390000], rate=80968.86/min -building interval tree based on /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=100000.00/min 
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[390000], rate=80136.99/min -building interval tree based on /tmp/nxf.FDhZqGVzDG/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 
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[390000], rate=77483.44/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 4800000.00 reads per min processed...  
 5000000.00 reads per min processed...  
 4500000.00 reads per min processed...  
 4666666.67 reads per min processed...  
 4800000.00 reads per min processed...  
 4909090.91 reads per min processed...  
 5000000.00 reads per min processed...  
 5076923.08 reads per min processed...  
 5142857.14 reads per min processed...  
 5200000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.FDhZqGVzDG/OvarianNP_FFPE_L02_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.FDhZqGVzDG/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -21147.988045
EM: Round [1] log likelihood: -21102.954752
EM: Round [2] log likelihood: -21082.030902
EM: Round [3] log likelihood: -21071.161116
EM: Round [4] log likelihood: -21065.172068
EM: Round [5] log likelihood: -21061.752354
EM: Round [6] log likelihood: -21059.739542
EM: Round [7] log likelihood: -21058.514895
EM: Round [8] log likelihood: -21057.742994
EM: Round [9] log likelihood: -21057.239168
EM: Round [10] log likelihood: -21056.899337
EM: Round [11] log likelihood: -21056.663107
EM: Round [12] log likelihood: -21056.494338
EM: Round [13] log likelihood: -21056.370747
EM: Round [14] log likelihood: -21056.278205
EM: Round [15] log likelihood: -21056.207518
EM: Round [16] log likelihood: -21056.152556
EM: Round [17] log likelihood: -21056.109141
EM: Round [18] log likelihood: -21056.074365
EM: Round [19] log likelihood: -21056.046166
EM: Round [20] log likelihood: -21056.023053
EM: Round [21] log likelihood: -21056.003930
EM: Round [22] log likelihood: -21055.987977
EM: Round [23] log likelihood: -21055.974575
EM: Round [24] log likelihood: -21055.963244
EM: Round [25] log likelihood: -21055.953614
EM: Round [26] log likelihood: -21055.945390
EM: Round [27] log likelihood: -21055.938337
EM: Round [28] log likelihood: -21055.932268
EM: Round [29] log likelihood: -21055.927027
EM: Round [30] log likelihood: -21055.922489
EM: Round [31] log likelihood: -21055.918549
EM: Round [32] log likelihood: -21055.915121
EM: Round [33] log likelihood: -21055.912132
EM: Round [34] log likelihood: -21055.909521
EM: Round [35] log likelihood: -21055.907235
EM: Round [36] log likelihood: -21055.905231
EM: Round [37] log likelihood: -21055.903472
EM: Round [38] log likelihood: -21055.901925
EM: Round [39] log likelihood: -21055.900563
EM: Round [40] log likelihood: -21055.899362
EM: Round [41] log likelihood: -21055.898302
EM: Round [42] log likelihood: -21055.897364
EM: Round [43] log likelihood: -21055.896535
EM: Round [44] log likelihood: -21055.895800
EM: Round [45] log likelihood: -21055.895148
EM: Round [46] log likelihood: -21055.894569
EM: Round [47] log likelihood: -21055.894054
EM: Round [48] log likelihood: -21055.893595
EM: Round [49] log likelihood: -21055.893187
EM: Round [50] log likelihood: -21055.892822
EM: Round [51] log likelihood: -21055.892497
EM: Round [52] log likelihood: -21055.892206
EM: Round [53] log likelihood: -21055.891946
EM: Round [54] log likelihood: -21055.891712
EM: Round [55] log likelihood: -21055.891503
EM: Round [56] log likelihood: -21055.891315
EM: Round [57] log likelihood: -21055.891146
EM: Round [58] log likelihood: -21055.890993
EM: Round [59] log likelihood: -21055.890856
EM: Round [60] log likelihood: -21055.890732
EM: Round [61] log likelihood: -21055.890620
EM: Round [62] log likelihood: -21055.890519
EM: Round [63] log likelihood: -21055.890428
EM: Stopping iterations at round 63 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -21136.372432
EM: Round [1] log likelihood: -21095.139128
EM: Round [2] log likelihood: -21076.816882
EM: Round [3] log likelihood: -21067.727148
EM: Round [4] log likelihood: -21062.894073
EM: Round [5] log likelihood: -21060.216696
EM: Round [6] log likelihood: -21058.684943
EM: Round [7] log likelihood: -21057.777235
EM: Round [8] log likelihood: -21057.218073
EM: Round [9] log likelihood: -21056.859708
EM: Round [10] log likelihood: -21056.621086
EM: Round [11] log likelihood: -21056.456421
EM: Round [12] log likelihood: -21056.339013
EM: Round [13] log likelihood: -21056.252788
EM: Round [14] log likelihood: -21056.187767
EM: Round [15] log likelihood: -21056.137579
EM: Round [16] log likelihood: -21056.098041
EM: Round [17] log likelihood: -21056.066340
EM: Round [18] log likelihood: -21056.040534
EM: Round [19] log likelihood: -21056.019258
EM: Round [20] log likelihood: -21056.001524
EM: Round [21] log likelihood: -21055.986608
EM: Round [22] log likelihood: -21055.973967
EM: Round [23] log likelihood: -21055.963185
EM: Round [24] log likelihood: -21055.953940
EM: Round [25] log likelihood: -21055.945978
EM: Round [26] log likelihood: -21055.939095
EM: Round [27] log likelihood: -21055.933125
EM: Round [28] log likelihood: -21055.927934
EM: Round [29] log likelihood: -21055.923410
EM: Round [30] log likelihood: -21055.919458
EM: Round [31] log likelihood: -21055.916000
EM: Round [32] log likelihood: -21055.912969
EM: Round [33] log likelihood: -21055.910310
EM: Round [34] log likelihood: -21055.907972
EM: Round [35] log likelihood: -21055.905915
EM: Round [36] log likelihood: -21055.904103
EM: Round [37] log likelihood: -21055.902505
EM: Round [38] log likelihood: -21055.901094
EM: Round [39] log likelihood: -21055.899847
EM: Round [40] log likelihood: -21055.898744
EM: Round [41] log likelihood: -21055.897766
EM: Round [42] log likelihood: -21055.896900
EM: Round [43] log likelihood: -21055.896131
EM: Round [44] log likelihood: -21055.895448
EM: Round [45] log likelihood: -21055.894841
EM: Round [46] log likelihood: -21055.894300
EM: Round [47] log likelihood: -21055.893819
EM: Round [48] log likelihood: -21055.893389
EM: Round [49] log likelihood: -21055.893006
EM: Round [50] log likelihood: -21055.892663
EM: Round [51] log likelihood: -21055.892357
EM: Round [52] log likelihood: -21055.892082
EM: Round [53] log likelihood: -21055.891836
EM: Round [54] log likelihood: -21055.891616
EM: Round [55] log likelihood: -21055.891417
EM: Round [56] log likelihood: -21055.891239
EM: Round [57] log likelihood: -21055.891078
EM: Round [58] log likelihood: -21055.890933
EM: Round [59] log likelihood: -21055.890802
EM: Round [60] log likelihood: -21055.890684
EM: Round [61] log likelihood: -21055.890578
EM: Round [62] log likelihood: -21055.890481
EM: Stopping iterations at round 62 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.FDhZqGVzDG/./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.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.FDhZqGVzDG/./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.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 12183393 > /tmp/nxf.FDhZqGVzDG/./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.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir > /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir --annotate /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.FDhZqGVzDG/./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.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir
-done, see /tmp/nxf.FDhZqGVzDG/./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.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.FDhZqGVzDG/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 159, filtered: 1853)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.FDhZqGVzDG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.FDhZqGVzDG/./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.FDhZqGVzDG/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 [ENSG00000259772.6]
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 [ENSG00000283122.1]
WARNING, no entry stored in dbm for [ENSG00000259768.6]
WARNING, no entry stored in dbm for [ENSG00000270972.1]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000279217.1]
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 [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 [ENSG00000197320.5]
WARNING, no entry stored in dbm for [ENSG00000277182.1]
WARNING, no entry stored in dbm for [ENSG00000236333.4]
WARNING, no entry stored in dbm for [ENSG00000281896.1]
WARNING, no entry stored in dbm for [ENSG00000240549.2]
WARNING, no entry stored in dbm for [ENSG00000277304.1]
WARNING, no entry stored in dbm for [ENSG00000226353.1]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000230936.1]
WARNING, no entry stored in dbm for [ENSG00000251889.1]
WARNING, no entry stored in dbm for [ENSG00000201806.1]
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 [ENSG00000223202.1]
WARNING, no entry stored in dbm for [ENSG00000200966.1]
WARNING, no entry stored in dbm for [ENSG00000287356.1]
WARNING, no entry stored in dbm for [ENSG00000238005.4]
WARNING, no entry stored in dbm for [ENSG00000226092.4]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000230082.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000255875.2]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000226029.1]
WARNING, no entry stored in dbm for [IGH-.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 [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 [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000203690.13]
WARNING, no entry stored in dbm for [ENSG00000236056.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000234766.2]
WARNING, no entry stored in dbm for [ENSG00000238164.6]
WARNING, no entry stored in dbm for [ENSG00000272235.1]
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 [IGL-.g@-ext]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000258680.2]
WARNING, no entry stored in dbm for [ENSG00000215067.10]
WARNING, no entry stored in dbm for [ENSG00000232217.1]
WARNING, no entry stored in dbm for [ENSG00000228685.1]
WARNING, no entry stored in dbm for [ENSG00000234851.4]
WARNING, no entry stored in dbm for [ENSG00000286215.1]
WARNING, no entry stored in dbm for [ENSG00000270522.1]
WARNING, no entry stored in dbm for [ENSG00000286641.1]
WARNING, no entry stored in dbm for [ENSG00000272449.2]
WARNING, no entry stored in dbm for [ENSG00000271913.7]
WARNING, no entry stored in dbm for [ENSG00000267515.1]
WARNING, no entry stored in dbm for [ENSG00000277332.1]
WARNING, no entry stored in dbm for [ENSG00000269292.1]
WARNING, no entry stored in dbm for [ENSG00000249685.1]
WARNING, no entry stored in dbm for [ENSG00000260693.1]
WARNING, no entry stored in dbm for [ENSG00000239533.6]
WARNING, no entry stored in dbm for [ENSG00000259952.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]


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