.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (rna_s1200_S21)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/e52eea2a2f14ee62984375d960c8cc/.command.log
Size: 20.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (rna_s1200_S21)
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/c2/50b83696c08fecc876ae36e6592660/rna_s1200_S21_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/e52eea2a2f14ee62984375d960c8cc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/e52eea2a2f14ee62984375d960c8cc/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/f995209d4716984aa8cac166d8a6b2/rna_s1200_S21.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/50b83696c08fecc876ae36e6592660/rna_s1200_S21_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.BgETZ3fqqA/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary
-sample contains 9937706 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir  -J /tmp/nxf.BgETZ3fqqA/rna_s1200_S21.Chimeric.out.junction  -O /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.BgETZ3fqqA/rna_s1200_S21.Chimeric.out.junction
-building interval tree based on /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=66666.67/min 
[20000], rate=66666.67/min 
[30000], rate=66666.67/min 
[40000], rate=66666.67/min 
[50000], rate=68181.82/min 
[60000], rate=70588.24/min -building interval tree based on /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes

[10000], rate=60000.00/min 
[20000], rate=70588.24/min 
[30000], rate=78260.87/min 
[40000], rate=70588.24/min 
[50000], rate=69767.44/min 
[60000], rate=69230.77/min -building interval tree based on /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes

[10000], rate=75000.00/min 
[20000], rate=66666.67/min 
[30000], rate=66666.67/min 
[40000], rate=64864.86/min 
[50000], rate=63829.79/min 
[60000], rate=63157.89/min -building interval tree based on /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes

[10000], rate=46153.85/min 
[20000], rate=46153.85/min 
[30000], rate=51428.57/min 
[40000], rate=53333.33/min 
[50000], rate=54545.45/min 
[60000], rate=58064.52/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 3000000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.BgETZ3fqqA/rna_s1200_S21.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.BgETZ3fqqA/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -21037.806319
EM: Round [1] log likelihood: -21027.151422
EM: Round [2] log likelihood: -21022.947708
EM: Round [3] log likelihood: -21020.808268
EM: Round [4] log likelihood: -21019.554654
EM: Round [5] log likelihood: -21018.752390
EM: Round [6] log likelihood: -21018.207583
EM: Round [7] log likelihood: -21017.821866
EM: Round [8] log likelihood: -21017.540419
EM: Round [9] log likelihood: -21017.330378
EM: Round [10] log likelihood: -21017.170868
EM: Round [11] log likelihood: -21017.048015
EM: Round [12] log likelihood: -21016.952272
EM: Round [13] log likelihood: -21016.876884
EM: Round [14] log likelihood: -21016.816977
EM: Round [15] log likelihood: -21016.768968
EM: Round [16] log likelihood: -21016.730194
EM: Round [17] log likelihood: -21016.698650
EM: Round [18] log likelihood: -21016.672810
EM: Round [19] log likelihood: -21016.651507
EM: Round [20] log likelihood: -21016.633839
EM: Round [21] log likelihood: -21016.619101
EM: Round [22] log likelihood: -21016.606744
EM: Round [23] log likelihood: -21016.596331
EM: Round [24] log likelihood: -21016.587516
EM: Round [25] log likelihood: -21016.580024
EM: Round [26] log likelihood: -21016.573631
EM: Round [27] log likelihood: -21016.568156
EM: Round [28] log likelihood: -21016.563452
EM: Round [29] log likelihood: -21016.559399
EM: Round [30] log likelihood: -21016.555897
EM: Round [31] log likelihood: -21016.552864
EM: Round [32] log likelihood: -21016.550232
EM: Round [33] log likelihood: -21016.547942
EM: Round [34] log likelihood: -21016.545946
EM: Round [35] log likelihood: -21016.544205
EM: Round [36] log likelihood: -21016.542682
EM: Round [37] log likelihood: -21016.541350
EM: Round [38] log likelihood: -21016.540182
EM: Round [39] log likelihood: -21016.539157
EM: Round [40] log likelihood: -21016.538257
EM: Round [41] log likelihood: -21016.537465
EM: Round [42] log likelihood: -21016.536769
EM: Round [43] log likelihood: -21016.536156
EM: Round [44] log likelihood: -21016.535616
EM: Round [45] log likelihood: -21016.535139
EM: Round [46] log likelihood: -21016.534719
EM: Round [47] log likelihood: -21016.534348
EM: Round [48] log likelihood: -21016.534020
EM: Round [49] log likelihood: -21016.533731
EM: Round [50] log likelihood: -21016.533475
EM: Round [51] log likelihood: -21016.533248
EM: Round [52] log likelihood: -21016.533048
EM: Round [53] log likelihood: -21016.532871
EM: Round [54] log likelihood: -21016.532714
EM: Round [55] log likelihood: -21016.532575
EM: Round [56] log likelihood: -21016.532452
EM: Round [57] log likelihood: -21016.532343
EM: Round [58] log likelihood: -21016.532246
EM: Stopping iterations at round 58 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -21035.098497
EM: Round [1] log likelihood: -21025.521070
EM: Round [2] log likelihood: -21021.946700
EM: Round [3] log likelihood: -21020.165161
EM: Round [4] log likelihood: -21019.123511
EM: Round [5] log likelihood: -21018.453443
EM: Round [6] log likelihood: -21017.995134
EM: Round [7] log likelihood: -21017.668271
EM: Round [8] log likelihood: -21017.428064
EM: Round [9] log likelihood: -21017.247536
EM: Round [10] log likelihood: -21017.109457
EM: Round [11] log likelihood: -21017.002326
EM: Round [12] log likelihood: -21016.918195
EM: Round [13] log likelihood: -21016.851425
EM: Round [14] log likelihood: -21016.797934
EM: Round [15] log likelihood: -21016.754713
EM: Round [16] log likelihood: -21016.719517
EM: Round [17] log likelihood: -21016.690649
EM: Round [18] log likelihood: -21016.666813
EM: Round [19] log likelihood: -21016.647012
EM: Round [20] log likelihood: -21016.630468
EM: Round [21] log likelihood: -21016.616574
EM: Round [22] log likelihood: -21016.604848
EM: Round [23] log likelihood: -21016.594909
EM: Round [24] log likelihood: -21016.586450
EM: Round [25] log likelihood: -21016.579225
EM: Round [26] log likelihood: -21016.573031
EM: Round [27] log likelihood: -21016.567706
EM: Round [28] log likelihood: -21016.563115
EM: Round [29] log likelihood: -21016.559146
EM: Round [30] log likelihood: -21016.555707
EM: Round [31] log likelihood: -21016.552722
EM: Round [32] log likelihood: -21016.550125
EM: Round [33] log likelihood: -21016.547862
EM: Round [34] log likelihood: -21016.545886
EM: Round [35] log likelihood: -21016.544160
EM: Round [36] log likelihood: -21016.542649
EM: Round [37] log likelihood: -21016.541324
EM: Round [38] log likelihood: -21016.540163
EM: Round [39] log likelihood: -21016.539143
EM: Round [40] log likelihood: -21016.538246
EM: Round [41] log likelihood: -21016.537457
EM: Round [42] log likelihood: -21016.536763
EM: Round [43] log likelihood: -21016.536151
EM: Round [44] log likelihood: -21016.535612
EM: Round [45] log likelihood: -21016.535137
EM: Round [46] log likelihood: -21016.534717
EM: Round [47] log likelihood: -21016.534346
EM: Round [48] log likelihood: -21016.534019
EM: Round [49] log likelihood: -21016.533730
EM: Round [50] log likelihood: -21016.533474
EM: Round [51] log likelihood: -21016.533248
EM: Round [52] log likelihood: -21016.533048
EM: Round [53] log likelihood: -21016.532870
EM: Round [54] log likelihood: -21016.532714
EM: Round [55] log likelihood: -21016.532575
EM: Round [56] log likelihood: -21016.532452
EM: Round [57] log likelihood: -21016.532343
EM: Round [58] log likelihood: -21016.532246
EM: Stopping iterations at round 58 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.BgETZ3fqqA/./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.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.BgETZ3fqqA/./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.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9937706 > /tmp/nxf.BgETZ3fqqA/./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.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir > /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir --annotate /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.BgETZ3fqqA/./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.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir
-done, see /tmp/nxf.BgETZ3fqqA/./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.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.BgETZ3fqqA/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 494, filtered: 1603)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.BgETZ3fqqA/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.BgETZ3fqqA/./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.BgETZ3fqqA/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
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WARNING, no entry stored in dbm for [ENSG00000262966.2]
WARNING, no entry stored in dbm for [ENSG00000265206.5]
WARNING, no entry stored in dbm for [ENSG00000265206.5]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [IGH-.g@-ext]


	* STAR-Fusion complete.  See output: /tmp/nxf.BgETZ3fqqA/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)