.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/00cd0d459bbfda626e5f66288ffdd6/.command.log
Size: 21.6 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1)
Attempt
Content

  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/9d/00cd0d459bbfda626e5f66288ffdd6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/00cd0d459bbfda626e5f66288ffdd6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/2c71724fed5339e4b5bf80f7876000/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/0545a1d7fc07e7ecb21450523058e8/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/0545a1d7fc07e7ecb21450523058e8/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.W9ly8IbBir/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary
-sample contains 6865293 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir  -J /tmp/nxf.W9ly8IbBir/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.W9ly8IbBir/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=54545.45/min 
[20000], rate=60000.00/min 
[30000], rate=54545.45/min 
[40000], rate=53333.33/min 
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[60000], rate=52173.91/min 
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[100000], rate=59405.94/min 
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[280000], rate=80000.00/min 
[290000], rate=78026.91/min 
[300000], rate=76595.74/min 
[310000], rate=76543.21/min -building interval tree based on /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=66666.67/min 
[20000], rate=75000.00/min 
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[310000], rate=69924.81/min -building interval tree based on /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=60000.00/min 
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[310000], rate=69402.99/min -building interval tree based on /tmp/nxf.W9ly8IbBir/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=85714.29/min 
[30000], rate=64285.71/min 
[40000], rate=61538.46/min 
[50000], rate=58823.53/min 
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[240000], rate=66666.67/min 
[250000], rate=66079.30/min 
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[280000], rate=66403.16/min 
[290000], rate=67181.47/min 
[300000], rate=67415.73/min 
[310000], rate=66666.67/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.W9ly8IbBir/./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...  
 4500000.00 reads per min processed...  
 4800000.00 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...  
 5454545.45 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.W9ly8IbBir/SkinN_FFPE_L01_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.W9ly8IbBir/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -18332.215194
EM: Round [1] log likelihood: -18309.904014
EM: Round [2] log likelihood: -18300.483976
EM: Round [3] log likelihood: -18295.704071
EM: Round [4] log likelihood: -18293.139671
EM: Round [5] log likelihood: -18291.720369
EM: Round [6] log likelihood: -18290.911896
EM: Round [7] log likelihood: -18290.436992
EM: Round [8] log likelihood: -18290.148792
EM: Round [9] log likelihood: -18289.967989
EM: Round [10] log likelihood: -18289.850813
EM: Round [11] log likelihood: -18289.772502
EM: Round [12] log likelihood: -18289.718655
EM: Round [13] log likelihood: -18289.680662
EM: Round [14] log likelihood: -18289.653220
EM: Round [15] log likelihood: -18289.632979
EM: Round [16] log likelihood: -18289.617764
EM: Round [17] log likelihood: -18289.606131
EM: Round [18] log likelihood: -18289.597101
EM: Round [19] log likelihood: -18289.589994
EM: Round [20] log likelihood: -18289.584332
EM: Round [21] log likelihood: -18289.579772
EM: Round [22] log likelihood: -18289.576063
EM: Round [23] log likelihood: -18289.573020
EM: Round [24] log likelihood: -18289.570503
EM: Round [25] log likelihood: -18289.568407
EM: Round [26] log likelihood: -18289.566650
EM: Round [27] log likelihood: -18289.565169
EM: Round [28] log likelihood: -18289.563914
EM: Round [29] log likelihood: -18289.562844
EM: Round [30] log likelihood: -18289.561930
EM: Round [31] log likelihood: -18289.561143
EM: Round [32] log likelihood: -18289.560465
EM: Round [33] log likelihood: -18289.559877
EM: Round [34] log likelihood: -18289.559367
EM: Round [35] log likelihood: -18289.558921
EM: Round [36] log likelihood: -18289.558531
EM: Round [37] log likelihood: -18289.558189
EM: Round [38] log likelihood: -18289.557887
EM: Round [39] log likelihood: -18289.557620
EM: Round [40] log likelihood: -18289.557383
EM: Round [41] log likelihood: -18289.557173
EM: Round [42] log likelihood: -18289.556986
EM: Round [43] log likelihood: -18289.556818
EM: Round [44] log likelihood: -18289.556668
EM: Round [45] log likelihood: -18289.556533
EM: Round [46] log likelihood: -18289.556411
EM: Round [47] log likelihood: -18289.556301
EM: Round [48] log likelihood: -18289.556201
EM: Stopping iterations at round 48 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -18329.002832
EM: Round [1] log likelihood: -18307.681754
EM: Round [2] log likelihood: -18299.092157
EM: Round [3] log likelihood: -18294.893890
EM: Round [4] log likelihood: -18292.687106
EM: Round [5] log likelihood: -18291.473096
EM: Round [6] log likelihood: -18290.778475
EM: Round [7] log likelihood: -18290.365740
EM: Round [8] log likelihood: -18290.111305
EM: Round [9] log likelihood: -18289.948818
EM: Round [10] log likelihood: -18289.841565
EM: Round [11] log likelihood: -18289.768600
EM: Round [12] log likelihood: -18289.717593
EM: Round [13] log likelihood: -18289.681057
EM: Round [14] log likelihood: -18289.654312
EM: Round [15] log likelihood: -18289.634352
EM: Round [16] log likelihood: -18289.619194
EM: Round [17] log likelihood: -18289.607502
EM: Round [18] log likelihood: -18289.598357
EM: Round [19] log likelihood: -18289.591114
EM: Round [20] log likelihood: -18289.585313
EM: Round [21] log likelihood: -18289.580619
EM: Round [22] log likelihood: -18289.576788
EM: Round [23] log likelihood: -18289.573636
EM: Round [24] log likelihood: -18289.571023
EM: Round [25] log likelihood: -18289.568843
EM: Round [26] log likelihood: -18289.567014
EM: Round [27] log likelihood: -18289.565471
EM: Round [28] log likelihood: -18289.564163
EM: Round [29] log likelihood: -18289.563049
EM: Round [30] log likelihood: -18289.562096
EM: Round [31] log likelihood: -18289.561278
EM: Round [32] log likelihood: -18289.560573
EM: Round [33] log likelihood: -18289.559964
EM: Round [34] log likelihood: -18289.559434
EM: Round [35] log likelihood: -18289.558973
EM: Round [36] log likelihood: -18289.558570
EM: Round [37] log likelihood: -18289.558217
EM: Round [38] log likelihood: -18289.557906
EM: Round [39] log likelihood: -18289.557633
EM: Round [40] log likelihood: -18289.557390
EM: Round [41] log likelihood: -18289.557175
EM: Round [42] log likelihood: -18289.556984
EM: Round [43] log likelihood: -18289.556813
EM: Round [44] log likelihood: -18289.556661
EM: Round [45] log likelihood: -18289.556524
EM: Round [46] log likelihood: -18289.556401
EM: Round [47] log likelihood: -18289.556290
EM: Round [48] log likelihood: -18289.556190
EM: Round [49] log likelihood: -18289.556099
EM: Stopping iterations at round 49 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.W9ly8IbBir/./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.W9ly8IbBir/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.W9ly8IbBir/./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.W9ly8IbBir/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 6865293 > /tmp/nxf.W9ly8IbBir/./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.W9ly8IbBir/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir > /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir --annotate /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.W9ly8IbBir/./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.W9ly8IbBir/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir
-done, see /tmp/nxf.W9ly8IbBir/./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.W9ly8IbBir/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.W9ly8IbBir/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 185, filtered: 1958)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.W9ly8IbBir/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.W9ly8IbBir/./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.W9ly8IbBir/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000251314.2]
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WARNING, no entry stored in dbm for [ENSG00000200475.1]
WARNING, no entry stored in dbm for [ENSG00000223117.1]
WARNING, no entry stored in dbm for [ENSG00000200830.1]
WARNING, no entry stored in dbm for [ENSG00000199691.1]
WARNING, no entry stored in dbm for [ENSG00000238247.2]
WARNING, no entry stored in dbm for [ENSG00000249937.8]
WARNING, no entry stored in dbm for [ENSG00000204055.5]
WARNING, no entry stored in dbm for [ENSG00000230461.9]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000288253.1]
WARNING, no entry stored in dbm for [ENSG00000204959.4]
WARNING, no entry stored in dbm for [ENSG00000259952.1]
WARNING, no entry stored in dbm for [ENSG00000231437.3]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000263753.8]
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 [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 [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 [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 [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000233837.1]
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 [ENSG00000251492.1]
WARNING, no entry stored in dbm for [ENSG00000281344.1]
WARNING, no entry stored in dbm for [ENSG00000174680.10]
WARNING, no entry stored in dbm for [ENSG00000230009.1]
WARNING, no entry stored in dbm for [ENSG00000257167.2]
WARNING, no entry stored in dbm for [ENSG00000198786.2]
WARNING, no entry stored in dbm for [ENSG00000244625.7]
WARNING, no entry stored in dbm for [ENSG00000230021.10]
WARNING, no entry stored in dbm for [ENSG00000213478.2]
WARNING, no entry stored in dbm for [ENSG00000249072.1]
WARNING, no entry stored in dbm for [ENSG00000229807.12]
WARNING, no entry stored in dbm for [ENSG00000254614.2]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
WARNING, no entry stored in dbm for [ENSG00000251562.8]
WARNING, no entry stored in dbm for [ENSG00000287979.1]
WARNING, no entry stored in dbm for [ENSG00000232748.3]
WARNING, no entry stored in dbm for [ENSG00000214999.3]


	* STAR-Fusion complete.  See output: /tmp/nxf.W9ly8IbBir/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)