.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (A549_FFPE_01_RNA_0001_B23LG7FLT4_3)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/4878303a2d40abedcaa0c6a66b5397/.command.log
Size: 15.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (A549_FFPE_01_RNA_0001_B23LG7FLT4_3)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/4e557baa29838aaa3a615aa612220e/A549_FFPE_01_RNA_0001_B23LG7FLT4_3_2.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/0e/ea93e46da6bd582932d770dbd03bfe/A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/4878303a2d40abedcaa0c6a66b5397/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/4878303a2d40abedcaa0c6a66b5397/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/4e557baa29838aaa3a615aa612220e/A549_FFPE_01_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.bgWrgwG1TR/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary
-sample contains 393174 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir  -J /tmp/nxf.bgWrgwG1TR/A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Chimeric.out.junction  -O /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.bgWrgwG1TR/A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Chimeric.out.junction
-building interval tree based on /tmp/nxf.bgWrgwG1TR/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 
[20000], rate=70588.24/min 
[30000], rate=78260.87/min 
[40000], rate=75000.00/min 
[50000], rate=75000.00/min 
[60000], rate=80000.00/min 
[70000], rate=76363.64/min 
[80000], rate=78688.52/min 
[90000], rate=76056.34/min 
[100000], rate=75949.37/min 
[110000], rate=75000.00/min 
[120000], rate=77419.35/min 
[130000], rate=80412.37/min 
[140000], rate=81553.40/min 
[150000], rate=83333.33/min -building interval tree based on /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=85714.29/min 
[20000], rate=70588.24/min 
[30000], rate=64285.71/min 
[40000], rate=68571.43/min 
[50000], rate=68181.82/min 
[60000], rate=70588.24/min 
[70000], rate=72413.79/min 
[80000], rate=71641.79/min 
[90000], rate=72972.97/min 
[100000], rate=73170.73/min 
[110000], rate=70212.77/min 
[120000], rate=69230.77/min 
[130000], rate=70270.27/min 
[140000], rate=71186.44/min 
[150000], rate=73170.73/min -building interval tree based on /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=42857.14/min 
[20000], rate=54545.45/min 
[30000], rate=64285.71/min 
[40000], rate=70588.24/min 
[50000], rate=73170.73/min 
[60000], rate=78260.87/min 
[70000], rate=65625.00/min 
[80000], rate=54545.45/min 
[90000], rate=55102.04/min 
[100000], rate=57142.86/min 
[110000], rate=59459.46/min 
[120000], rate=62068.97/min 
[130000], rate=62903.23/min 
[140000], rate=63636.36/min 
[150000], rate=63829.79/min -building interval tree based on /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=33333.33/min 
[20000], rate=37500.00/min 
[30000], rate=47368.42/min 
[40000], rate=51063.83/min 
[50000], rate=56603.77/min 
[60000], rate=60000.00/min 
[70000], rate=60869.57/min 
[80000], rate=60000.00/min 
[90000], rate=59340.66/min 
[100000], rate=60606.06/min 
[110000], rate=61682.24/min 
[120000], rate=58536.59/min 
[130000], rate=57777.78/min 
[140000], rate=57534.25/min 
[150000], rate=57324.84/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.bgWrgwG1TR/./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...  
 6000000.00 reads per min processed...  
 5000000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.bgWrgwG1TR/A549_FFPE_01_RNA_0001_B23LG7FLT4_3.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.bgWrgwG1TR/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -3871.825438
EM: Round [1] log likelihood: -3868.713469
EM: Round [2] log likelihood: -3867.549277
EM: Round [3] log likelihood: -3867.029987
EM: Round [4] log likelihood: -3866.776838
EM: Round [5] log likelihood: -3866.646027
EM: Round [6] log likelihood: -3866.575052
EM: Round [7] log likelihood: -3866.534664
EM: Round [8] log likelihood: -3866.510537
EM: Round [9] log likelihood: -3866.495407
EM: Round [10] log likelihood: -3866.485471
EM: Round [11] log likelihood: -3866.478672
EM: Round [12] log likelihood: -3866.473856
EM: Round [13] log likelihood: -3866.470349
EM: Round [14] log likelihood: -3866.467738
EM: Round [15] log likelihood: -3866.465764
EM: Round [16] log likelihood: -3866.464251
EM: Round [17] log likelihood: -3866.463082
EM: Round [18] log likelihood: -3866.462173
EM: Round [19] log likelihood: -3866.461461
EM: Round [20] log likelihood: -3866.460901
EM: Round [21] log likelihood: -3866.460460
EM: Round [22] log likelihood: -3866.460112
EM: Round [23] log likelihood: -3866.459835
EM: Round [24] log likelihood: -3866.459616
EM: Round [25] log likelihood: -3866.459442
EM: Round [26] log likelihood: -3866.459304
EM: Round [27] log likelihood: -3866.459194
EM: Round [28] log likelihood: -3866.459106
EM: Stopping iterations at round 28 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -3871.566018
EM: Round [1] log likelihood: -3868.607804
EM: Round [2] log likelihood: -3867.505963
EM: Round [3] log likelihood: -3867.012373
EM: Round [4] log likelihood: -3866.769724
EM: Round [5] log likelihood: -3866.643166
EM: Round [6] log likelihood: -3866.573904
EM: Round [7] log likelihood: -3866.534204
EM: Round [8] log likelihood: -3866.510353
EM: Round [9] log likelihood: -3866.495333
EM: Round [10] log likelihood: -3866.485441
EM: Round [11] log likelihood: -3866.478660
EM: Round [12] log likelihood: -3866.473851
EM: Round [13] log likelihood: -3866.470347
EM: Round [14] log likelihood: -3866.467738
EM: Round [15] log likelihood: -3866.465763
EM: Round [16] log likelihood: -3866.464251
EM: Round [17] log likelihood: -3866.463082
EM: Round [18] log likelihood: -3866.462173
EM: Round [19] log likelihood: -3866.461461
EM: Round [20] log likelihood: -3866.460901
EM: Round [21] log likelihood: -3866.460460
EM: Round [22] log likelihood: -3866.460112
EM: Round [23] log likelihood: -3866.459835
EM: Round [24] log likelihood: -3866.459616
EM: Round [25] log likelihood: -3866.459442
EM: Round [26] log likelihood: -3866.459304
EM: Round [27] log likelihood: -3866.459194
EM: Round [28] log likelihood: -3866.459106
EM: Stopping iterations at round 28 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.bgWrgwG1TR/./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.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.bgWrgwG1TR/./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.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 393174 > /tmp/nxf.bgWrgwG1TR/./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.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir > /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir --annotate /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.bgWrgwG1TR/./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.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir
-done, see /tmp/nxf.bgWrgwG1TR/./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.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.bgWrgwG1TR/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 38, filtered: 566)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.bgWrgwG1TR/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.bgWrgwG1TR/./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.bgWrgwG1TR/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGL-.g@-ext]
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	* STAR-Fusion complete.  See output: /tmp/nxf.bgWrgwG1TR/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)