.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-2482ef-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/e79f9697fba74169fa9cbb277b765e/.command.log
Size: 22.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-2482ef-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/43c796e110bfab5220c82c2e6e1af2/aih-tih-sc-2482ef-R1_A23WJ53LT4_1_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/71/7f0b12c243fdf8cbd636ce9eb410d9/aih-tih-sc-2482ef-R1_A23WJ53LT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/e79f9697fba74169fa9cbb277b765e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/e79f9697fba74169fa9cbb277b765e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/43c796e110bfab5220c82c2e6e1af2/aih-tih-sc-2482ef-R1_A23WJ53LT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.xpWA506MIv/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.xpWA506MIv/./star-fusion.preliminary
-sample contains 30565238 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir  -J /tmp/nxf.xpWA506MIv/aih-tih-sc-2482ef-R1_A23WJ53LT4_1.Chimeric.out.junction  -O /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.xpWA506MIv/aih-tih-sc-2482ef-R1_A23WJ53LT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[360000], rate=68789.81/min -building interval tree based on /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[360000], rate=65060.24/min -building interval tree based on /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[350000], rate=58495.82/min -building interval tree based on /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[360000], rate=56396.87/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 0.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 4800000.00 reads per min processed...  
 4285714.29 reads per min processed...  
 4000000.00 reads per min processed...  
 4200000.00 reads per min processed...  
 4363636.36 reads per min processed...  
 4153846.15 reads per min processed...  
 4285714.29 reads per min processed...  
 4125000.00 reads per min processed...  
 4235294.12 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.xpWA506MIv/aih-tih-sc-2482ef-R1_A23WJ53LT4_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.xpWA506MIv/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -30411.583639
EM: Round [1] log likelihood: -30391.074954
EM: Round [2] log likelihood: -30382.212396
EM: Round [3] log likelihood: -30377.544250
EM: Round [4] log likelihood: -30374.960347
EM: Round [5] log likelihood: -30373.519741
EM: Round [6] log likelihood: -30372.711250
EM: Round [7] log likelihood: -30372.250618
EM: Round [8] log likelihood: -30371.981836
EM: Round [9] log likelihood: -30371.820226
EM: Round [10] log likelihood: -30371.719803
EM: Round [11] log likelihood: -30371.655296
EM: Round [12] log likelihood: -30371.612536
EM: Round [13] log likelihood: -30371.583375
EM: Round [14] log likelihood: -30371.562985
EM: Round [15] log likelihood: -30371.548423
EM: Round [16] log likelihood: -30371.537836
EM: Round [17] log likelihood: -30371.530024
EM: Round [18] log likelihood: -30371.524188
EM: Round [19] log likelihood: -30371.519785
EM: Round [20] log likelihood: -30371.516433
EM: Round [21] log likelihood: -30371.513865
EM: Round [22] log likelihood: -30371.511884
EM: Round [23] log likelihood: -30371.510350
EM: Round [24] log likelihood: -30371.509156
EM: Round [25] log likelihood: -30371.508224
EM: Round [26] log likelihood: -30371.507494
EM: Round [27] log likelihood: -30371.506920
EM: Round [28] log likelihood: -30371.506469
EM: Round [29] log likelihood: -30371.506113
EM: Round [30] log likelihood: -30371.505832
EM: Round [31] log likelihood: -30371.505610
EM: Round [32] log likelihood: -30371.505434
EM: Round [33] log likelihood: -30371.505294
EM: Round [34] log likelihood: -30371.505183
EM: Round [35] log likelihood: -30371.505095
EM: Stopping iterations at round 35 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -30398.097994
EM: Round [1] log likelihood: -30379.514831
EM: Round [2] log likelihood: -30371.556467
EM: Round [3] log likelihood: -30367.438386
EM: Round [4] log likelihood: -30365.207028
EM: Round [5] log likelihood: -30363.985742
EM: Round [6] log likelihood: -30363.306834
EM: Round [7] log likelihood: -30362.919677
EM: Round [8] log likelihood: -30362.691602
EM: Round [9] log likelihood: -30362.552341
EM: Round [10] log likelihood: -30362.464185
EM: Round [11] log likelihood: -30362.406440
EM: Round [12] log likelihood: -30362.367432
EM: Round [13] log likelihood: -30362.340367
EM: Round [14] log likelihood: -30362.321158
EM: Round [15] log likelihood: -30362.307265
EM: Round [16] log likelihood: -30362.297060
EM: Round [17] log likelihood: -30362.289467
EM: Round [18] log likelihood: -30362.283758
EM: Round [19] log likelihood: -30362.279427
EM: Round [20] log likelihood: -30362.276119
EM: Round [21] log likelihood: -30362.273575
EM: Round [22] log likelihood: -30362.271610
EM: Round [23] log likelihood: -30362.270084
EM: Round [24] log likelihood: -30362.268895
EM: Round [25] log likelihood: -30362.267966
EM: Round [26] log likelihood: -30362.267238
EM: Round [27] log likelihood: -30362.266666
EM: Round [28] log likelihood: -30362.266215
EM: Round [29] log likelihood: -30362.265860
EM: Round [30] log likelihood: -30362.265579
EM: Round [31] log likelihood: -30362.265356
EM: Round [32] log likelihood: -30362.265180
EM: Round [33] log likelihood: -30362.265041
EM: Round [34] log likelihood: -30362.264930
EM: Round [35] log likelihood: -30362.264842
EM: Stopping iterations at round 35 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.xpWA506MIv/./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.xpWA506MIv/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.xpWA506MIv/./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.xpWA506MIv/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 30565238 > /tmp/nxf.xpWA506MIv/./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.xpWA506MIv/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir > /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir --annotate /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.xpWA506MIv/./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.xpWA506MIv/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir
-done, see /tmp/nxf.xpWA506MIv/./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.xpWA506MIv/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.xpWA506MIv/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 355, filtered: 2825)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.xpWA506MIv/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.xpWA506MIv/./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.xpWA506MIv/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
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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 [ENSG00000259917.1]
WARNING, no entry stored in dbm for [ENSG00000204622.11]
WARNING, no entry stored in dbm for [ENSG00000235290.1]
WARNING, no entry stored in dbm for [ENSG00000260827.1]
WARNING, no entry stored in dbm for [ENSG00000204529.4]
WARNING, no entry stored in dbm for [ENSG00000255345.1]
WARNING, no entry stored in dbm for [ENSG00000234741.8]
WARNING, no entry stored in dbm for [ENSG00000255471.1]
WARNING, no entry stored in dbm for [ENSG00000170919.16]
WARNING, no entry stored in dbm for [ENSG00000265735.2]
WARNING, no entry stored in dbm for [ENSG00000276168.1]
WARNING, no entry stored in dbm for [ENSG00000213090.2]
WARNING, no entry stored in dbm for [ENSG00000249252.5]
WARNING, no entry stored in dbm for [ENSG00000235963.1]
WARNING, no entry stored in dbm for [ENSG00000236360.2]
WARNING, no entry stored in dbm for [ENSG00000174680.10]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000178722.13]
WARNING, no entry stored in dbm for [ENSG00000178722.13]
WARNING, no entry stored in dbm for [ENSG00000245261.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000255118.1]
WARNING, no entry stored in dbm for [ENSG00000196756.13]
WARNING, no entry stored in dbm for [ENSG00000255980.1]
WARNING, no entry stored in dbm for [ENSG00000269516.6]
WARNING, no entry stored in dbm for [ENSG00000262943.7]
WARNING, no entry stored in dbm for [ENSG00000282885.2]
WARNING, no entry stored in dbm for [ENSG00000241082.3]
WARNING, no entry stored in dbm for [ENSG00000275046.1]
WARNING, no entry stored in dbm for [ENSG00000235020.5]
WARNING, no entry stored in dbm for [ENSG00000286215.1]
WARNING, no entry stored in dbm for [ENSG00000220685.3]
WARNING, no entry stored in dbm for [ENSG00000233183.3]
WARNING, no entry stored in dbm for [ENSG00000287346.1]
WARNING, no entry stored in dbm for [ENSG00000279933.1]
WARNING, no entry stored in dbm for [ENSG00000215022.7]
WARNING, no entry stored in dbm for [ENSG00000231760.5]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000285668.1]
WARNING, no entry stored in dbm for [ENSG00000235421.1]
WARNING, no entry stored in dbm for [ENSG00000262580.5]
WARNING, no entry stored in dbm for [ENSG00000280707.2]
WARNING, no entry stored in dbm for [ENSG00000243144.7]
WARNING, no entry stored in dbm for [ENSG00000228434.1]
WARNING, no entry stored in dbm for [ENSG00000259299.1]
WARNING, no entry stored in dbm for [ENSG00000259299.1]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000243289.1]
WARNING, no entry stored in dbm for [ENSG00000271382.1]
WARNING, no entry stored in dbm for [ENSG00000268460.2]
WARNING, no entry stored in dbm for [ENSG00000285523.1]
WARNING, no entry stored in dbm for [ENSG00000241057.2]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000212663.2]
WARNING, no entry stored in dbm for [ENSG00000267698.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.xpWA506MIv/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)