.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (dna_s739)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/493d39c3f55c27513e6172b9d32c70/.command.log
Size: 16.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (dna_s739)
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/fa/493d39c3f55c27513e6172b9d32c70/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/53af804381e3eae521f5a4f9552428/dna_s739.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/493d39c3f55c27513e6172b9d32c70/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/8fac7d2ec09eeabc5dba0d598e1c86/dna_s739_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/8fac7d2ec09eeabc5dba0d598e1c86/dna_s739_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.9F9wSOHPJX/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary
-sample contains 7383040 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir  -J /tmp/nxf.9F9wSOHPJX/dna_s739.Chimeric.out.junction  -O /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.9F9wSOHPJX/dna_s739.Chimeric.out.junction
-building interval tree based on /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=50000.00/min 
[20000], rate=52173.91/min 
[30000], rate=58064.52/min 
[40000], rate=54545.45/min 
[50000], rate=50847.46/min 
[60000], rate=49315.07/min 
[70000], rate=48275.86/min 
[80000], rate=46153.85/min 
[90000], rate=45000.00/min 
[100000], rate=45112.78/min 
[110000], rate=45833.33/min 
[120000], rate=45283.02/min 
[130000], rate=45086.71/min 
[140000], rate=44680.85/min 
[150000], rate=43478.26/min 
[160000], rate=43049.33/min 
[170000], rate=43220.34/min 
[180000], rate=43724.70/min -building interval tree based on /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=66666.67/min 
[20000], rate=63157.89/min 
[30000], rate=62068.97/min 
[40000], rate=70588.24/min 
[50000], rate=69767.44/min 
[60000], rate=59016.39/min 
[70000], rate=48837.21/min 
[80000], rate=44859.81/min 
[90000], rate=44628.10/min 
[100000], rate=45112.78/min 
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[130000], rate=41489.36/min 
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[150000], rate=39823.01/min 
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[170000], rate=38636.36/min 
[180000], rate=38434.16/min -building interval tree based on /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=54545.45/min 
[20000], rate=46153.85/min 
[30000], rate=43902.44/min 
[40000], rate=45283.02/min 
[50000], rate=44776.12/min 
[60000], rate=42857.14/min 
[70000], rate=42424.24/min 
[80000], rate=40000.00/min 
[90000], rate=39416.06/min 
[100000], rate=40268.46/min 
[110000], rate=41250.00/min 
[120000], rate=38918.92/min 
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[140000], rate=35443.04/min 
[150000], rate=32374.10/min 
[160000], rate=31578.95/min 
[170000], rate=31677.02/min 
[180000], rate=31858.41/min -building interval tree based on /tmp/nxf.9F9wSOHPJX/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 
[20000], rate=23529.41/min 
[30000], rate=22784.81/min 
[40000], rate=22222.22/min 
[50000], rate=23622.05/min 
[60000], rate=25352.11/min 
[70000], rate=27272.73/min 
[80000], rate=27906.98/min 
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[100000], rate=29556.65/min 
[110000], rate=28205.13/min 
[120000], rate=28015.56/min 
[130000], rate=28782.29/min 
[140000], rate=28865.98/min 
[150000], rate=28571.43/min 
[160000], rate=29003.02/min 
[170000], rate=29737.61/min 
[180000], rate=30422.54/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 2000000.00 reads per min processed...  
 2400000.00 reads per min processed...  
 2571428.57 reads per min processed...  
 3000000.00 reads per min processed...  
 3000000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.9F9wSOHPJX/dna_s739.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.9F9wSOHPJX/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -19923.093750
EM: Round [1] log likelihood: -19918.497089
EM: Round [2] log likelihood: -19916.693581
EM: Round [3] log likelihood: -19915.823110
EM: Round [4] log likelihood: -19915.366059
EM: Round [5] log likelihood: -19915.120841
EM: Round [6] log likelihood: -19914.988729
EM: Round [7] log likelihood: -19914.917125
EM: Round [8] log likelihood: -19914.877859
EM: Round [9] log likelihood: -19914.855969
EM: Round [10] log likelihood: -19914.843530
EM: Round [11] log likelihood: -19914.836314
EM: Round [12] log likelihood: -19914.832041
EM: Round [13] log likelihood: -19914.829460
EM: Round [14] log likelihood: -19914.827874
EM: Round [15] log likelihood: -19914.826884
EM: Round [16] log likelihood: -19914.826257
EM: Round [17] log likelihood: -19914.825856
EM: Round [18] log likelihood: -19914.825596
EM: Round [19] log likelihood: -19914.825428
EM: Round [20] log likelihood: -19914.825318
EM: Round [21] log likelihood: -19914.825245
EM: Stopping iterations at round 21 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -19922.336064
EM: Round [1] log likelihood: -19917.837620
EM: Round [2] log likelihood: -19916.219848
EM: Round [3] log likelihood: -19915.525456
EM: Round [4] log likelihood: -19915.195939
EM: Round [5] log likelihood: -19915.029294
EM: Round [6] log likelihood: -19914.941148
EM: Round [7] log likelihood: -19914.892857
EM: Round [8] log likelihood: -19914.865601
EM: Round [9] log likelihood: -19914.849810
EM: Round [10] log likelihood: -19914.840442
EM: Round [11] log likelihood: -19914.834768
EM: Round [12] log likelihood: -19914.831267
EM: Round [13] log likelihood: -19914.829074
EM: Round [14] log likelihood: -19914.827681
EM: Round [15] log likelihood: -19914.826787
EM: Round [16] log likelihood: -19914.826208
EM: Round [17] log likelihood: -19914.825831
EM: Round [18] log likelihood: -19914.825584
EM: Round [19] log likelihood: -19914.825422
EM: Round [20] log likelihood: -19914.825315
EM: Round [21] log likelihood: -19914.825244
EM: Stopping iterations at round 21 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 7383040 > /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir > /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir --annotate /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir
-done, see /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 204, filtered: 2570)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000276088.1]
WARNING, no entry stored in dbm for [ENSG00000282458.1]
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WARNING, no entry stored in dbm for [ENSG00000242593.7]


	* STAR-Fusion complete.  See output: /tmp/nxf.9F9wSOHPJX/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)