.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-331e97-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/88ad062ea12add83edbd2914e0ba30/.command.log
Size: 13.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-331e97-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/a0d557773d3a9c2b740f3684069b86/aih-tih-sc-331e97-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/51/43d0eeeb57f6e794c1328833b6aa50/aih-tih-sc-331e97-R1_A23WJ53LT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/88ad062ea12add83edbd2914e0ba30/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/88ad062ea12add83edbd2914e0ba30/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/a0d557773d3a9c2b740f3684069b86/aih-tih-sc-331e97-R1_A23WJ53LT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.mMHlTwZpc9/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary
-sample contains 698690 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir  -J /tmp/nxf.mMHlTwZpc9/aih-tih-sc-331e97-R1_A23WJ53LT4_1.Chimeric.out.junction  -O /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.mMHlTwZpc9/aih-tih-sc-331e97-R1_A23WJ53LT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=75000.00/min -building interval tree based on /tmp/nxf.mMHlTwZpc9/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 -building interval tree based on /tmp/nxf.mMHlTwZpc9/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 -building interval tree based on /tmp/nxf.mMHlTwZpc9/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 * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.mMHlTwZpc9/aih-tih-sc-331e97-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.mMHlTwZpc9/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -1128.259930
EM: Round [1] log likelihood: -1127.619008
EM: Round [2] log likelihood: -1127.384714
EM: Round [3] log likelihood: -1127.283659
EM: Round [4] log likelihood: -1127.236538
EM: Round [5] log likelihood: -1127.212797
EM: Round [6] log likelihood: -1127.199682
EM: Round [7] log likelihood: -1127.191582
EM: Round [8] log likelihood: -1127.185939
EM: Round [9] log likelihood: -1127.181558
EM: Round [10] log likelihood: -1127.177872
EM: Round [11] log likelihood: -1127.174610
EM: Round [12] log likelihood: -1127.171642
EM: Round [13] log likelihood: -1127.168905
EM: Round [14] log likelihood: -1127.166370
EM: Round [15] log likelihood: -1127.164018
EM: Round [16] log likelihood: -1127.161841
EM: Round [17] log likelihood: -1127.159830
EM: Round [18] log likelihood: -1127.157979
EM: Round [19] log likelihood: -1127.156279
EM: Round [20] log likelihood: -1127.154723
EM: Round [21] log likelihood: -1127.153303
EM: Round [22] log likelihood: -1127.152010
EM: Round [23] log likelihood: -1127.150835
EM: Round [24] log likelihood: -1127.149771
EM: Round [25] log likelihood: -1127.148808
EM: Round [26] log likelihood: -1127.147939
EM: Round [27] log likelihood: -1127.147156
EM: Round [28] log likelihood: -1127.146451
EM: Round [29] log likelihood: -1127.145817
EM: Round [30] log likelihood: -1127.145248
EM: Round [31] log likelihood: -1127.144738
EM: Round [32] log likelihood: -1127.144281
EM: Round [33] log likelihood: -1127.143871
EM: Round [34] log likelihood: -1127.143505
EM: Round [35] log likelihood: -1127.143178
EM: Round [36] log likelihood: -1127.142886
EM: Round [37] log likelihood: -1127.142624
EM: Round [38] log likelihood: -1127.142392
EM: Round [39] log likelihood: -1127.142184
EM: Round [40] log likelihood: -1127.141998
EM: Round [41] log likelihood: -1127.141833
EM: Round [42] log likelihood: -1127.141686
EM: Round [43] log likelihood: -1127.141555
EM: Round [44] log likelihood: -1127.141438
EM: Round [45] log likelihood: -1127.141334
EM: Round [46] log likelihood: -1127.141241
EM: Stopping iterations at round 46 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -1128.138774
EM: Round [1] log likelihood: -1127.567580
EM: Round [2] log likelihood: -1127.359583
EM: Round [3] log likelihood: -1127.270195
EM: Round [4] log likelihood: -1127.228604
EM: Round [5] log likelihood: -1127.207581
EM: Round [6] log likelihood: -1127.195844
EM: Round [7] log likelihood: -1127.188472
EM: Round [8] log likelihood: -1127.183242
EM: Round [9] log likelihood: -1127.179121
EM: Round [10] log likelihood: -1127.175623
EM: Round [11] log likelihood: -1127.172514
EM: Round [12] log likelihood: -1127.169684
EM: Round [13] log likelihood: -1127.167078
EM: Round [14] log likelihood: -1127.164668
EM: Round [15] log likelihood: -1127.162439
EM: Round [16] log likelihood: -1127.160380
EM: Round [17] log likelihood: -1127.158483
EM: Round [18] log likelihood: -1127.156741
EM: Round [19] log likelihood: -1127.155145
EM: Round [20] log likelihood: -1127.153688
EM: Round [21] log likelihood: -1127.152360
EM: Round [22] log likelihood: -1127.151153
EM: Round [23] log likelihood: -1127.150059
EM: Round [24] log likelihood: -1127.149068
EM: Round [25] log likelihood: -1127.148174
EM: Round [26] log likelihood: -1127.147367
EM: Round [27] log likelihood: -1127.146641
EM: Round [28] log likelihood: -1127.145988
EM: Round [29] log likelihood: -1127.145401
EM: Round [30] log likelihood: -1127.144875
EM: Round [31] log likelihood: -1127.144404
EM: Round [32] log likelihood: -1127.143982
EM: Round [33] log likelihood: -1127.143604
EM: Round [34] log likelihood: -1127.143266
EM: Round [35] log likelihood: -1127.142964
EM: Round [36] log likelihood: -1127.142695
EM: Round [37] log likelihood: -1127.142454
EM: Round [38] log likelihood: -1127.142240
EM: Round [39] log likelihood: -1127.142048
EM: Round [40] log likelihood: -1127.141878
EM: Round [41] log likelihood: -1127.141726
EM: Round [42] log likelihood: -1127.141590
EM: Round [43] log likelihood: -1127.141469
EM: Round [44] log likelihood: -1127.141362
EM: Round [45] log likelihood: -1127.141266
EM: Stopping iterations at round 45 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 698690 > /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir > /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir --annotate /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir
-done, see /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 23, filtered: 272)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000251562.8]
WARNING, no entry stored in dbm for [ENSG00000251562.8]
WARNING, no entry stored in dbm for [ENSG00000260735.2]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000233955.1]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000260236.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.mMHlTwZpc9/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)