.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/39a2fa3f2cdf61ca20bc9828d09c98/.command.log
Size: 22.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/9d987c5c8df046f7f4a619e267e157/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_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/dd/9d987c5c8df046f7f4a619e267e157/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/9432b492030b76af3248c3b7e8a412/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/39a2fa3f2cdf61ca20bc9828d09c98/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/39a2fa3f2cdf61ca20bc9828d09c98/.command.run
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.Xm4ZXcMiae/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary
-sample contains 11357275 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir  -J /tmp/nxf.Xm4ZXcMiae/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction  -O /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.Xm4ZXcMiae/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=46153.85/min 
[20000], rate=54545.45/min 
[30000], rate=48648.65/min 
[40000], rate=51063.83/min 
[50000], rate=49180.33/min 
[60000], rate=48648.65/min 
[70000], rate=50000.00/min 
[80000], rate=51612.90/min 
[90000], rate=51923.08/min 
[100000], rate=53097.35/min 
[110000], rate=53658.54/min 
[120000], rate=54135.34/min 
[130000], rate=54545.45/min -building interval tree based on /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=50000.00/min 
[20000], rate=41379.31/min 
[30000], rate=43902.44/min 
[40000], rate=47058.82/min 
[50000], rate=50000.00/min 
[60000], rate=51428.57/min 
[70000], rate=53164.56/min 
[80000], rate=54545.45/min 
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[100000], rate=56603.77/min 
[110000], rate=54545.45/min 
[120000], rate=53333.33/min 
[130000], rate=53061.22/min 
[140000], rate=53503.18/min -building interval tree based on /tmp/nxf.Xm4ZXcMiae/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=66666.67/min 
[40000], rate=68571.43/min 
[50000], rate=52631.58/min 
[60000], rate=46753.25/min 
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[90000], rate=47787.61/min 
[100000], rate=48780.49/min 
[110000], rate=47482.01/min 
[120000], rate=47682.12/min 
[130000], rate=48447.20/min -building interval tree based on /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=35294.12/min 
[20000], rate=42857.14/min 
[30000], rate=43902.44/min 
[40000], rate=42857.14/min 
[50000], rate=42253.52/min 
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[80000], rate=40336.13/min 
[90000], rate=39416.06/min 
[100000], rate=38961.04/min 
[110000], rate=39520.96/min 
[120000], rate=38297.87/min 
[130000], rate=38048.78/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

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

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.Xm4ZXcMiae/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_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.Xm4ZXcMiae/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -138658.210881
EM: Round [1] log likelihood: -138651.960466
EM: Round [2] log likelihood: -138649.415565
EM: Round [3] log likelihood: -138648.070307
EM: Round [4] log likelihood: -138647.288930
EM: Round [5] log likelihood: -138646.816484
EM: Round [6] log likelihood: -138646.518837
EM: Round [7] log likelihood: -138646.321088
EM: Round [8] log likelihood: -138646.182225
EM: Round [9] log likelihood: -138646.079921
EM: Round [10] log likelihood: -138646.001692
EM: Round [11] log likelihood: -138645.940191
EM: Round [12] log likelihood: -138645.890839
EM: Round [13] log likelihood: -138645.850615
EM: Round [14] log likelihood: -138645.817432
EM: Round [15] log likelihood: -138645.789793
EM: Round [16] log likelihood: -138645.766592
EM: Round [17] log likelihood: -138645.746988
EM: Round [18] log likelihood: -138645.730336
EM: Round [19] log likelihood: -138645.716125
EM: Round [20] log likelihood: -138645.703952
EM: Round [21] log likelihood: -138645.693488
EM: Round [22] log likelihood: -138645.684469
EM: Round [23] log likelihood: -138645.676676
EM: Round [24] log likelihood: -138645.669928
EM: Round [25] log likelihood: -138645.664074
EM: Round [26] log likelihood: -138645.658987
EM: Round [27] log likelihood: -138645.654561
EM: Round [28] log likelihood: -138645.650704
EM: Round [29] log likelihood: -138645.647340
EM: Round [30] log likelihood: -138645.644403
EM: Round [31] log likelihood: -138645.641836
EM: Round [32] log likelihood: -138645.639591
EM: Round [33] log likelihood: -138645.637626
EM: Round [34] log likelihood: -138645.635905
EM: Round [35] log likelihood: -138645.634396
EM: Round [36] log likelihood: -138645.633073
EM: Round [37] log likelihood: -138645.631912
EM: Round [38] log likelihood: -138645.630892
EM: Round [39] log likelihood: -138645.629997
EM: Round [40] log likelihood: -138645.629210
EM: Round [41] log likelihood: -138645.628518
EM: Round [42] log likelihood: -138645.627909
EM: Round [43] log likelihood: -138645.627374
EM: Round [44] log likelihood: -138645.626902
EM: Round [45] log likelihood: -138645.626487
EM: Round [46] log likelihood: -138645.626121
EM: Round [47] log likelihood: -138645.625799
EM: Round [48] log likelihood: -138645.625515
EM: Round [49] log likelihood: -138645.625264
EM: Round [50] log likelihood: -138645.625043
EM: Round [51] log likelihood: -138645.624848
EM: Round [52] log likelihood: -138645.624676
EM: Round [53] log likelihood: -138645.624524
EM: Round [54] log likelihood: -138645.624389
EM: Round [55] log likelihood: -138645.624271
EM: Round [56] log likelihood: -138645.624166
EM: Round [57] log likelihood: -138645.624073
EM: Stopping iterations at round 57 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -138656.954309
EM: Round [1] log likelihood: -138651.440517
EM: Round [2] log likelihood: -138649.191124
EM: Round [3] log likelihood: -138647.971797
EM: Round [4] log likelihood: -138647.245387
EM: Round [5] log likelihood: -138646.797179
EM: Round [6] log likelihood: -138646.510266
EM: Round [7] log likelihood: -138646.317280
EM: Round [8] log likelihood: -138646.180533
EM: Round [9] log likelihood: -138646.079169
EM: Round [10] log likelihood: -138646.001358
EM: Round [11] log likelihood: -138645.940043
EM: Round [12] log likelihood: -138645.890773
EM: Round [13] log likelihood: -138645.850585
EM: Round [14] log likelihood: -138645.817419
EM: Round [15] log likelihood: -138645.789787
EM: Round [16] log likelihood: -138645.766589
EM: Round [17] log likelihood: -138645.746987
EM: Round [18] log likelihood: -138645.730336
EM: Round [19] log likelihood: -138645.716125
EM: Round [20] log likelihood: -138645.703952
EM: Round [21] log likelihood: -138645.693488
EM: Round [22] log likelihood: -138645.684469
EM: Round [23] log likelihood: -138645.676676
EM: Round [24] log likelihood: -138645.669928
EM: Round [25] log likelihood: -138645.664074
EM: Round [26] log likelihood: -138645.658987
EM: Round [27] log likelihood: -138645.654561
EM: Round [28] log likelihood: -138645.650704
EM: Round [29] log likelihood: -138645.647340
EM: Round [30] log likelihood: -138645.644403
EM: Round [31] log likelihood: -138645.641836
EM: Round [32] log likelihood: -138645.639591
EM: Round [33] log likelihood: -138645.637626
EM: Round [34] log likelihood: -138645.635905
EM: Round [35] log likelihood: -138645.634396
EM: Round [36] log likelihood: -138645.633073
EM: Round [37] log likelihood: -138645.631912
EM: Round [38] log likelihood: -138645.630892
EM: Round [39] log likelihood: -138645.629997
EM: Round [40] log likelihood: -138645.629210
EM: Round [41] log likelihood: -138645.628518
EM: Round [42] log likelihood: -138645.627909
EM: Round [43] log likelihood: -138645.627374
EM: Round [44] log likelihood: -138645.626902
EM: Round [45] log likelihood: -138645.626487
EM: Round [46] log likelihood: -138645.626121
EM: Round [47] log likelihood: -138645.625799
EM: Round [48] log likelihood: -138645.625515
EM: Round [49] log likelihood: -138645.625264
EM: Round [50] log likelihood: -138645.625043
EM: Round [51] log likelihood: -138645.624848
EM: Round [52] log likelihood: -138645.624676
EM: Round [53] log likelihood: -138645.624524
EM: Round [54] log likelihood: -138645.624389
EM: Round [55] log likelihood: -138645.624271
EM: Round [56] log likelihood: -138645.624166
EM: Round [57] log likelihood: -138645.624073
EM: Stopping iterations at round 57 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.Xm4ZXcMiae/./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.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.Xm4ZXcMiae/./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.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 11357275 > /tmp/nxf.Xm4ZXcMiae/./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.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir > /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir --annotate /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.Xm4ZXcMiae/./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.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir
-done, see /tmp/nxf.Xm4ZXcMiae/./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.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.Xm4ZXcMiae/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 579, filtered: 6836)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.Xm4ZXcMiae/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.Xm4ZXcMiae/./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.Xm4ZXcMiae/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
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WARNING, no entry stored in dbm for [ENSG00000271394.1]
WARNING, no entry stored in dbm for [ENSG00000237080.3]
WARNING, no entry stored in dbm for [ENSG00000254635.6]
WARNING, no entry stored in dbm for [ENSG00000100058.12]
WARNING, no entry stored in dbm for [ENSG00000233997.5]
WARNING, no entry stored in dbm for [ENSG00000246695.8]
WARNING, no entry stored in dbm for [ENSG00000235038.1]
WARNING, no entry stored in dbm for [ENSG00000277449.1]
WARNING, no entry stored in dbm for [ENSG00000218418.2]
WARNING, no entry stored in dbm for [ENSG00000250591.3]
WARNING, no entry stored in dbm for [ENSG00000226445.2]
WARNING, no entry stored in dbm for [ENSG00000233871.2]
WARNING, no entry stored in dbm for [ENSG00000205534.6]
WARNING, no entry stored in dbm for [ENSG00000271699.5]
WARNING, no entry stored in dbm for [ENSG00000284543.1]
WARNING, no entry stored in dbm for [ENSG00000241859.7]
WARNING, no entry stored in dbm for [ENSG00000230021.10]
WARNING, no entry stored in dbm for [ENSG00000230021.10]
WARNING, no entry stored in dbm for [ENSG00000286215.1]
WARNING, no entry stored in dbm for [ENSG00000241494.1]
WARNING, no entry stored in dbm for [ENSG00000250140.1]
WARNING, no entry stored in dbm for [ENSG00000233457.1]
WARNING, no entry stored in dbm for [ENSG00000233178.7]
WARNING, no entry stored in dbm for [ENSG00000230615.7]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000247775.2]
WARNING, no entry stored in dbm for [ENSG00000249306.6]
WARNING, no entry stored in dbm for [ENSG00000278638.2]
WARNING, no entry stored in dbm for [ENSG00000268034.1]
WARNING, no entry stored in dbm for [ENSG00000275807.1]
WARNING, no entry stored in dbm for [ENSG00000278212.2]
WARNING, no entry stored in dbm for [ENSG00000219410.6]
WARNING, no entry stored in dbm for [ENSG00000267665.2]
WARNING, no entry stored in dbm for [ENSG00000235881.2]
WARNING, no entry stored in dbm for [ENSG00000278791.1]
WARNING, no entry stored in dbm for [ENSG00000278791.1]
WARNING, no entry stored in dbm for [ENSG00000228981.3]
WARNING, no entry stored in dbm for [ENSG00000251378.1]
WARNING, no entry stored in dbm for [ENSG00000233184.7]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000266283.1]
WARNING, no entry stored in dbm for [ENSG00000250938.6]
WARNING, no entry stored in dbm for [ENSG00000286171.1]
WARNING, no entry stored in dbm for [ENSG00000272693.4]
WARNING, no entry stored in dbm for [ENSG00000283390.1]
WARNING, no entry stored in dbm for [ENSG00000185641.6]
WARNING, no entry stored in dbm for [ENSG00000188002.10]
WARNING, no entry stored in dbm for [ENSG00000204876.4]
WARNING, no entry stored in dbm for [ENSG00000249406.3]
WARNING, no entry stored in dbm for [ENSG00000227307.1]
WARNING, no entry stored in dbm for [ENSG00000230383.1]
WARNING, no entry stored in dbm for [ENSG00000260905.1]
WARNING, no entry stored in dbm for [ENSG00000197332.9]
WARNING, no entry stored in dbm for [ENSG00000230305.2]


	* STAR-Fusion complete.  See output: /tmp/nxf.Xm4ZXcMiae/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)