.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/8ead042c314bc869b453eabe2c00ed/.command.err
Size: 20.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1)
Attempt
Content

-ctat genome lib [/tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.Yp32mmEtW3/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary
-sample contains 9544799 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir  -J /tmp/nxf.Yp32mmEtW3/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.Yp32mmEtW3/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes

[10000], rate=100000.00/min 
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[360000], rate=79120.88/min -building interval tree based on /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=54545.45/min 
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[100000], rate=80000.00/min 
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[370000], rate=76816.61/min -building interval tree based on /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=150000.00/min 
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[360000], rate=77142.86/min -building interval tree based on /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes

[10000], rate=60000.00/min 
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[360000], rate=72972.97/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 0.00 reads per min processed...  
 12000000.00 reads per min processed...  
 9000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 5250000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 5500000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.Yp32mmEtW3/BreastNP_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.Yp32mmEtW3/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -27663.761920
EM: Round [1] log likelihood: -27627.378741
EM: Round [2] log likelihood: -27610.234343
EM: Round [3] log likelihood: -27601.166966
EM: Round [4] log likelihood: -27596.162532
EM: Round [5] log likelihood: -27593.351991
EM: Round [6] log likelihood: -27591.748107
EM: Round [7] log likelihood: -27590.811780
EM: Round [8] log likelihood: -27590.249281
EM: Round [9] log likelihood: -27589.900505
EM: Round [10] log likelihood: -27589.677141
EM: Round [11] log likelihood: -27589.529472
EM: Round [12] log likelihood: -27589.428814
EM: Round [13] log likelihood: -27589.358184
EM: Round [14] log likelihood: -27589.307261
EM: Round [15] log likelihood: -27589.269616
EM: Round [16] log likelihood: -27589.241145
EM: Round [17] log likelihood: -27589.219166
EM: Round [18] log likelihood: -27589.201886
EM: Round [19] log likelihood: -27589.188082
EM: Round [20] log likelihood: -27589.176901
EM: Round [21] log likelihood: -27589.167736
EM: Round [22] log likelihood: -27589.160148
EM: Round [23] log likelihood: -27589.153810
EM: Round [24] log likelihood: -27589.148478
EM: Round [25] log likelihood: -27589.143966
EM: Round [26] log likelihood: -27589.140126
EM: Round [27] log likelihood: -27589.136846
EM: Round [28] log likelihood: -27589.134032
EM: Round [29] log likelihood: -27589.131611
EM: Round [30] log likelihood: -27589.129522
EM: Round [31] log likelihood: -27589.127715
EM: Round [32] log likelihood: -27589.126148
EM: Round [33] log likelihood: -27589.124787
EM: Round [34] log likelihood: -27589.123602
EM: Round [35] log likelihood: -27589.122569
EM: Round [36] log likelihood: -27589.121667
EM: Round [37] log likelihood: -27589.120878
EM: Round [38] log likelihood: -27589.120186
EM: Round [39] log likelihood: -27589.119579
EM: Round [40] log likelihood: -27589.119045
EM: Round [41] log likelihood: -27589.118575
EM: Round [42] log likelihood: -27589.118160
EM: Round [43] log likelihood: -27589.117793
EM: Round [44] log likelihood: -27589.117469
EM: Round [45] log likelihood: -27589.117181
EM: Round [46] log likelihood: -27589.116925
EM: Round [47] log likelihood: -27589.116698
EM: Round [48] log likelihood: -27589.116494
EM: Round [49] log likelihood: -27589.116313
EM: Round [50] log likelihood: -27589.116150
EM: Round [51] log likelihood: -27589.116004
EM: Round [52] log likelihood: -27589.115872
EM: Round [53] log likelihood: -27589.115754
EM: Round [54] log likelihood: -27589.115646
EM: Round [55] log likelihood: -27589.115549
EM: Stopping iterations at round 55 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -27655.239467
EM: Round [1] log likelihood: -27622.229560
EM: Round [2] log likelihood: -27607.074371
EM: Round [3] log likelihood: -27599.169079
EM: Round [4] log likelihood: -27594.877067
EM: Round [5] log likelihood: -27592.510620
EM: Round [6] log likelihood: -27591.185061
EM: Round [7] log likelihood: -27590.425506
EM: Round [8] log likelihood: -27589.977637
EM: Round [9] log likelihood: -27589.704943
EM: Round [10] log likelihood: -27589.533238
EM: Round [11] log likelihood: -27589.421404
EM: Round [12] log likelihood: -27589.346110
EM: Round [13] log likelihood: -27589.293779
EM: Round [14] log likelihood: -27589.256305
EM: Round [15] log likelihood: -27589.228718
EM: Round [16] log likelihood: -27589.207898
EM: Round [17] log likelihood: -27589.191831
EM: Round [18] log likelihood: -27589.179190
EM: Round [19] log likelihood: -27589.169076
EM: Round [20] log likelihood: -27589.160867
EM: Round [21] log likelihood: -27589.154125
EM: Round [22] log likelihood: -27589.148531
EM: Round [23] log likelihood: -27589.143850
EM: Round [24] log likelihood: -27589.139907
EM: Round [25] log likelihood: -27589.136564
EM: Round [26] log likelihood: -27589.133718
EM: Round [27] log likelihood: -27589.131284
EM: Round [28] log likelihood: -27589.129195
EM: Round [29] log likelihood: -27589.127396
EM: Round [30] log likelihood: -27589.125844
EM: Round [31] log likelihood: -27589.124502
EM: Round [32] log likelihood: -27589.123337
EM: Round [33] log likelihood: -27589.122325
EM: Round [34] log likelihood: -27589.121444
EM: Round [35] log likelihood: -27589.120676
EM: Round [36] log likelihood: -27589.120004
EM: Round [37] log likelihood: -27589.119416
EM: Round [38] log likelihood: -27589.118900
EM: Round [39] log likelihood: -27589.118447
EM: Round [40] log likelihood: -27589.118048
EM: Round [41] log likelihood: -27589.117695
EM: Round [42] log likelihood: -27589.117384
EM: Round [43] log likelihood: -27589.117108
EM: Round [44] log likelihood: -27589.116863
EM: Round [45] log likelihood: -27589.116645
EM: Round [46] log likelihood: -27589.116450
EM: Round [47] log likelihood: -27589.116276
EM: Round [48] log likelihood: -27589.116121
EM: Round [49] log likelihood: -27589.115981
EM: Round [50] log likelihood: -27589.115854
EM: Round [51] log likelihood: -27589.115741
EM: Round [52] log likelihood: -27589.115637
EM: Round [53] log likelihood: -27589.115544
EM: Stopping iterations at round 53 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.Yp32mmEtW3/./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.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.Yp32mmEtW3/./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.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9544799 > /tmp/nxf.Yp32mmEtW3/./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.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir > /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir --annotate /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.Yp32mmEtW3/./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.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir
-done, see /tmp/nxf.Yp32mmEtW3/./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.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.Yp32mmEtW3/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 211, filtered: 2681)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.Yp32mmEtW3/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.Yp32mmEtW3/./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.Yp32mmEtW3/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000181577.16]
WARNING, no entry stored in dbm for [ENSG00000224286.6]
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WARNING, no entry stored in dbm for [ENSG00000265962.1]
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WARNING, no entry stored in dbm for [ENSG00000249072.1]
WARNING, no entry stored in dbm for [ENSG00000232732.11]
WARNING, no entry stored in dbm for [ENSG00000254254.6]
WARNING, no entry stored in dbm for [ENSG00000285045.1]
WARNING, no entry stored in dbm for [ENSG00000255399.4]
WARNING, no entry stored in dbm for [ENSG00000213371.4]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000161912.18]
WARNING, no entry stored in dbm for [ENSG00000287356.1]
WARNING, no entry stored in dbm for [ENSG00000287356.1]
WARNING, no entry stored in dbm for [ENSG00000287356.1]
WARNING, no entry stored in dbm for [ENSG00000181577.16]
WARNING, no entry stored in dbm for [ENSG00000278040.1]
WARNING, no entry stored in dbm for [ENSG00000220472.1]
WARNING, no entry stored in dbm for [ENSG00000230387.4]
WARNING, no entry stored in dbm for [ENSG00000280011.1]
WARNING, no entry stored in dbm for [ENSG00000231672.8]
WARNING, no entry stored in dbm for [ENSG00000279047.4]
WARNING, no entry stored in dbm for [ENSG00000278131.1]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000268729.1]
WARNING, no entry stored in dbm for [ENSG00000233539.5]
WARNING, no entry stored in dbm for [ENSG00000263499.1]
WARNING, no entry stored in dbm for [ENSG00000236531.2]
WARNING, no entry stored in dbm for [ENSG00000279655.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.Yp32mmEtW3/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)