.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BVT_FFPE_TRNA_utn_01_A23WKFTLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/56a066fa4302761058e08335fae93a/.command.log
Size: 19.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BVT_FFPE_TRNA_utn_01_A23WKFTLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/f4fb901400f9fe707dc716a44e54a7/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_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/06/f4fb901400f9fe707dc716a44e54a7/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/56a066fa4302761058e08335fae93a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/56a066fa4302761058e08335fae93a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/9bcade78bb83eeb32cad6a1515ee9d/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.ud4o2VMoq5/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary
-sample contains 14109910 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir  -J /tmp/nxf.ud4o2VMoq5/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_1.Chimeric.out.junction  -O /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.ud4o2VMoq5/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=60000.00/min 
[20000], rate=70588.24/min 
[30000], rate=60000.00/min 
[40000], rate=57142.86/min 
[50000], rate=57692.31/min 
[60000], rate=61016.95/min 
[70000], rate=63636.36/min 
[80000], rate=62337.66/min 
[90000], rate=61363.64/min 
[100000], rate=61855.67/min 
[110000], rate=63461.54/min 
[120000], rate=63716.81/min 
[130000], rate=61904.76/min 
[140000], rate=61764.71/min 
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[160000], rate=63576.16/min 
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[180000], rate=63157.89/min 
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[200000], rate=63829.79/min 
[210000], rate=63959.39/min 
[220000], rate=64705.88/min 
[230000], rate=64788.73/min 
[240000], rate=64573.99/min 
[250000], rate=65217.39/min -building interval tree based on /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=46153.85/min 
[20000], rate=48000.00/min 
[30000], rate=50000.00/min 
[40000], rate=53333.33/min 
[50000], rate=57692.31/min 
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[70000], rate=60869.57/min 
[80000], rate=61538.46/min 
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[100000], rate=65217.39/min 
[110000], rate=68750.00/min 
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[200000], rate=65217.39/min 
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[230000], rate=63594.47/min 
[240000], rate=64000.00/min 
[250000], rate=63559.32/min -building interval tree based on /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=46153.85/min 
[20000], rate=52173.91/min 
[30000], rate=60000.00/min 
[40000], rate=60000.00/min 
[50000], rate=56603.77/min 
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[240000], rate=61802.58/min 
[250000], rate=62500.00/min -building interval tree based on /tmp/nxf.ud4o2VMoq5/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=109090.91/min 
[30000], rate=100000.00/min 
[40000], rate=72727.27/min 
[50000], rate=57692.31/min 
[60000], rate=51428.57/min 
[70000], rate=48275.86/min 
[80000], rate=48000.00/min 
[90000], rate=47787.61/min 
[100000], rate=48780.49/min 
[110000], rate=50381.68/min 
[120000], rate=52173.91/min 
[130000], rate=52702.70/min 
[140000], rate=53503.18/min 
[150000], rate=54545.45/min 
[160000], rate=56140.35/min 
[170000], rate=56666.67/min 
[180000], rate=55670.10/min 
[190000], rate=55072.46/min 
[200000], rate=55045.87/min 
[210000], rate=54545.45/min 
[220000], rate=53877.55/min 
[230000], rate=53906.25/min 
[240000], rate=53932.58/min 
[250000], rate=54744.53/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 6000000.00 reads per min processed...  
 4000000.00 reads per min processed...  
 4500000.00 reads per min processed...  
 4000000.00 reads per min processed...  
 3750000.00 reads per min processed...  
 4000000.00 reads per min processed...  
 3818181.82 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.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.ud4o2VMoq5/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_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.ud4o2VMoq5/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -23823.559661
EM: Round [1] log likelihood: -23816.533258
EM: Round [2] log likelihood: -23813.873371
EM: Round [3] log likelihood: -23812.650039
EM: Round [4] log likelihood: -23812.053195
EM: Round [5] log likelihood: -23811.754431
EM: Round [6] log likelihood: -23811.601826
EM: Round [7] log likelihood: -23811.522258
EM: Round [8] log likelihood: -23811.479869
EM: Round [9] log likelihood: -23811.456785
EM: Round [10] log likelihood: -23811.443937
EM: Round [11] log likelihood: -23811.436630
EM: Round [12] log likelihood: -23811.432389
EM: Round [13] log likelihood: -23811.429881
EM: Round [14] log likelihood: -23811.428370
EM: Round [15] log likelihood: -23811.427447
EM: Round [16] log likelihood: -23811.426874
EM: Round [17] log likelihood: -23811.426516
EM: Round [18] log likelihood: -23811.426288
EM: Round [19] log likelihood: -23811.426143
EM: Round [20] log likelihood: -23811.426050
EM: Stopping iterations at round 20 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -23820.261910
EM: Round [1] log likelihood: -23814.955980
EM: Round [2] log likelihood: -23813.073659
EM: Round [3] log likelihood: -23812.242612
EM: Round [4] log likelihood: -23811.846962
EM: Round [5] log likelihood: -23811.650688
EM: Round [6] log likelihood: -23811.549849
EM: Round [7] log likelihood: -23811.496275
EM: Round [8] log likelihood: -23811.466896
EM: Round [9] log likelihood: -23811.450313
EM: Round [10] log likelihood: -23811.440709
EM: Round [11] log likelihood: -23811.435021
EM: Round [12] log likelihood: -23811.431588
EM: Round [13] log likelihood: -23811.429482
EM: Round [14] log likelihood: -23811.428172
EM: Round [15] log likelihood: -23811.427349
EM: Round [16] log likelihood: -23811.426826
EM: Round [17] log likelihood: -23811.426492
EM: Round [18] log likelihood: -23811.426277
EM: Round [19] log likelihood: -23811.426138
EM: Round [20] log likelihood: -23811.426047
EM: Stopping iterations at round 20 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.ud4o2VMoq5/./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.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.ud4o2VMoq5/./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.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 14109910 > /tmp/nxf.ud4o2VMoq5/./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.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir > /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir --annotate /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.ud4o2VMoq5/./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.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir
-done, see /tmp/nxf.ud4o2VMoq5/./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.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.ud4o2VMoq5/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 316, filtered: 2601)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.ud4o2VMoq5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.ud4o2VMoq5/./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.ud4o2VMoq5/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000198786.2]
WARNING, no entry stored in dbm for [ENSG00000245958.6]
WARNING, no entry stored in dbm for [ENSG00000229638.1]
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WARNING, no entry stored in dbm for [ENSG00000198786.2]
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WARNING, no entry stored in dbm for [ENSG00000249257.1]
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WARNING, no entry stored in dbm for [ENSG00000257696.1]
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WARNING, no entry stored in dbm for [ENSG00000267469.1]
WARNING, no entry stored in dbm for [ENSG00000235852.1]
WARNING, no entry stored in dbm for [ENSG00000285486.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.ud4o2VMoq5/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)