.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/53b45c8371fa6a43fcad7c6ab2352b/.command.log
Size: 18.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/15963dba4d935ffd3d52b93bfc4e41/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/ac109c0031aa049abdc246b4535984/1173_QEV_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/ae/53b45c8371fa6a43fcad7c6ab2352b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/53b45c8371fa6a43fcad7c6ab2352b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/ac109c0031aa049abdc246b4535984/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.0jMiK3qXRn/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary
-sample contains 9824221 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir  -J /tmp/nxf.0jMiK3qXRn/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction  -O /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.0jMiK3qXRn/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=37500.00/min 
[20000], rate=40000.00/min 
[30000], rate=36734.69/min 
[40000], rate=38709.68/min 
[50000], rate=41666.67/min 
[60000], rate=43902.44/min 
[70000], rate=46153.85/min 
[80000], rate=51063.83/min 
[90000], rate=54000.00/min 
[100000], rate=58823.53/min 
[110000], rate=62857.14/min 
[120000], rate=63716.81/min 
[130000], rate=67826.09/min 
[140000], rate=69421.49/min 
[150000], rate=71428.57/min 
[160000], rate=72180.45/min 
[170000], rate=75000.00/min 
[180000], rate=78832.12/min 
[190000], rate=77551.02/min -building interval tree based on /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=40000.00/min 
[20000], rate=37500.00/min 
[30000], rate=39130.43/min 
[40000], rate=42105.26/min 
[50000], rate=42253.52/min 
[60000], rate=44444.44/min 
[70000], rate=44680.85/min 
[80000], rate=46153.85/min 
[90000], rate=46153.85/min 
[100000], rate=46153.85/min 
[110000], rate=46808.51/min 
[120000], rate=48000.00/min 
[130000], rate=48447.20/min 
[140000], rate=49122.81/min 
[150000], rate=48648.65/min 
[160000], rate=49484.54/min 
[170000], rate=51000.00/min 
[180000], rate=51428.57/min 
[190000], rate=53023.26/min -building interval tree based on /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=75000.00/min 
[20000], rate=85714.29/min 
[30000], rate=94736.84/min 
[40000], rate=92307.69/min 
[50000], rate=107142.86/min 
[60000], rate=102857.14/min 
[70000], rate=102439.02/min 
[80000], rate=100000.00/min 
[90000], rate=100000.00/min 
[100000], rate=85714.29/min 
[110000], rate=70967.74/min 
[120000], rate=63716.81/min 
[130000], rate=60937.50/min 
[140000], rate=60869.57/min 
[150000], rate=60000.00/min 
[160000], rate=57831.33/min 
[170000], rate=54838.71/min 
[180000], rate=52682.93/min 
[190000], rate=52293.58/min -building interval tree based on /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=33333.33/min 
[20000], rate=38709.68/min 
[30000], rate=43902.44/min 
[40000], rate=45283.02/min 
[50000], rate=47619.05/min 
[60000], rate=47368.42/min 
[70000], rate=47191.01/min 
[80000], rate=46601.94/min 
[90000], rate=45762.71/min 
[100000], rate=45112.78/min 
[110000], rate=46478.87/min 
[120000], rate=45859.87/min 
[130000], rate=45348.84/min 
[140000], rate=44444.44/min 
[150000], rate=44117.65/min 
[160000], rate=45070.42/min 
[170000], rate=46363.64/min 
[180000], rate=45378.15/min 
[190000], rate=44881.89/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 3000000.00 reads per min processed...  
 3000000.00 reads per min processed...  
 3000000.00 reads per min processed...  
 3428571.43 reads per min processed...  
 3333333.33 reads per min processed...  
 3600000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.0jMiK3qXRn/1173_QEV_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.0jMiK3qXRn/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -11852.442008
EM: Round [1] log likelihood: -11823.350898
EM: Round [2] log likelihood: -11810.332441
EM: Round [3] log likelihood: -11803.439017
EM: Round [4] log likelihood: -11799.644918
EM: Round [5] log likelihood: -11797.524680
EM: Round [6] log likelihood: -11796.312173
EM: Round [7] log likelihood: -11795.595375
EM: Round [8] log likelihood: -11795.155118
EM: Round [9] log likelihood: -11794.874127
EM: Round [10] log likelihood: -11794.688266
EM: Round [11] log likelihood: -11794.561345
EM: Round [12] log likelihood: -11794.472216
EM: Round [13] log likelihood: -11794.408079
EM: Round [14] log likelihood: -11794.360924
EM: Round [15] log likelihood: -11794.325586
EM: Round [16] log likelihood: -11794.298640
EM: Round [17] log likelihood: -11794.277761
EM: Round [18] log likelihood: -11794.261337
EM: Round [19] log likelihood: -11794.248233
EM: Round [20] log likelihood: -11794.237632
EM: Round [21] log likelihood: -11794.228941
EM: Round [22] log likelihood: -11794.221726
EM: Round [23] log likelihood: -11794.215661
EM: Round [24] log likelihood: -11794.210502
EM: Round [25] log likelihood: -11794.206064
EM: Round [26] log likelihood: -11794.202205
EM: Round [27] log likelihood: -11794.198817
EM: Round [28] log likelihood: -11794.195814
EM: Round [29] log likelihood: -11794.193130
EM: Round [30] log likelihood: -11794.190712
EM: Round [31] log likelihood: -11794.188519
EM: Round [32] log likelihood: -11794.186517
EM: Round [33] log likelihood: -11794.184680
EM: Round [34] log likelihood: -11794.182986
EM: Round [35] log likelihood: -11794.181418
EM: Round [36] log likelihood: -11794.179959
EM: Round [37] log likelihood: -11794.178599
EM: Round [38] log likelihood: -11794.177328
EM: Round [39] log likelihood: -11794.176136
EM: Round [40] log likelihood: -11794.175017
EM: Round [41] log likelihood: -11794.173963
EM: Round [42] log likelihood: -11794.172971
EM: Round [43] log likelihood: -11794.172035
EM: Round [44] log likelihood: -11794.171151
EM: Round [45] log likelihood: -11794.170316
EM: Round [46] log likelihood: -11794.169526
EM: Round [47] log likelihood: -11794.168778
EM: Round [48] log likelihood: -11794.168070
EM: Round [49] log likelihood: -11794.167399
EM: Round [50] log likelihood: -11794.166763
EM: Round [51] log likelihood: -11794.166161
EM: Round [52] log likelihood: -11794.165589
EM: Round [53] log likelihood: -11794.165047
EM: Round [54] log likelihood: -11794.164532
EM: Round [55] log likelihood: -11794.164044
EM: Round [56] log likelihood: -11794.163581
EM: Round [57] log likelihood: -11794.163142
EM: Round [58] log likelihood: -11794.162725
EM: Round [59] log likelihood: -11794.162329
EM: Round [60] log likelihood: -11794.161953
EM: Round [61] log likelihood: -11794.161596
EM: Round [62] log likelihood: -11794.161257
EM: Round [63] log likelihood: -11794.160935
EM: Round [64] log likelihood: -11794.160629
EM: Round [65] log likelihood: -11794.160339
EM: Round [66] log likelihood: -11794.160063
EM: Round [67] log likelihood: -11794.159801
EM: Round [68] log likelihood: -11794.159552
EM: Round [69] log likelihood: -11794.159316
EM: Round [70] log likelihood: -11794.159091
EM: Round [71] log likelihood: -11794.158878
EM: Round [72] log likelihood: -11794.158675
EM: Round [73] log likelihood: -11794.158483
EM: Round [74] log likelihood: -11794.158300
EM: Round [75] log likelihood: -11794.158126
EM: Round [76] log likelihood: -11794.157960
EM: Round [77] log likelihood: -11794.157803
EM: Round [78] log likelihood: -11794.157654
EM: Round [79] log likelihood: -11794.157511
EM: Round [80] log likelihood: -11794.157376
EM: Round [81] log likelihood: -11794.157248
EM: Round [82] log likelihood: -11794.157125
EM: Round [83] log likelihood: -11794.157009
EM: Round [84] log likelihood: -11794.156898
EM: Round [85] log likelihood: -11794.156793
EM: Round [86] log likelihood: -11794.156693
EM: Round [87] log likelihood: -11794.156598
EM: Stopping iterations at round 87 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -11847.597142
EM: Round [1] log likelihood: -11819.634612
EM: Round [2] log likelihood: -11807.834418
EM: Round [3] log likelihood: -11801.909458
EM: Round [4] log likelihood: -11798.728317
EM: Round [5] log likelihood: -11796.960972
EM: Round [6] log likelihood: -11795.947512
EM: Round [7] log likelihood: -11795.345047
EM: Round [8] log likelihood: -11794.972983
EM: Round [9] log likelihood: -11794.734585
EM: Round [10] log likelihood: -11794.576637
EM: Round [11] log likelihood: -11794.468869
EM: Round [12] log likelihood: -11794.393443
EM: Round [13] log likelihood: -11794.339476
EM: Round [14] log likelihood: -11794.300113
EM: Round [15] log likelihood: -11794.270911
EM: Round [16] log likelihood: -11794.248914
EM: Round [17] log likelihood: -11794.232111
EM: Round [18] log likelihood: -11794.219110
EM: Round [19] log likelihood: -11794.208928
EM: Round [20] log likelihood: -11794.200861
EM: Round [21] log likelihood: -11794.194399
EM: Round [22] log likelihood: -11794.189168
EM: Round [23] log likelihood: -11794.184890
EM: Round [24] log likelihood: -11794.181356
EM: Round [25] log likelihood: -11794.178409
EM: Round [26] log likelihood: -11794.175929
EM: Round [27] log likelihood: -11794.173823
EM: Round [28] log likelihood: -11794.172020
EM: Round [29] log likelihood: -11794.170463
EM: Round [30] log likelihood: -11794.169108
EM: Round [31] log likelihood: -11794.167921
EM: Round [32] log likelihood: -11794.166873
EM: Round [33] log likelihood: -11794.165943
EM: Round [34] log likelihood: -11794.165113
EM: Round [35] log likelihood: -11794.164367
EM: Round [36] log likelihood: -11794.163694
EM: Round [37] log likelihood: -11794.163084
EM: Round [38] log likelihood: -11794.162529
EM: Round [39] log likelihood: -11794.162022
EM: Round [40] log likelihood: -11794.161557
EM: Round [41] log likelihood: -11794.161130
EM: Round [42] log likelihood: -11794.160736
EM: Round [43] log likelihood: -11794.160372
EM: Round [44] log likelihood: -11794.160036
EM: Round [45] log likelihood: -11794.159723
EM: Round [46] log likelihood: -11794.159433
EM: Round [47] log likelihood: -11794.159163
EM: Round [48] log likelihood: -11794.158911
EM: Round [49] log likelihood: -11794.158676
EM: Round [50] log likelihood: -11794.158456
EM: Round [51] log likelihood: -11794.158251
EM: Round [52] log likelihood: -11794.158059
EM: Round [53] log likelihood: -11794.157879
EM: Round [54] log likelihood: -11794.157710
EM: Round [55] log likelihood: -11794.157552
EM: Round [56] log likelihood: -11794.157403
EM: Round [57] log likelihood: -11794.157263
EM: Round [58] log likelihood: -11794.157132
EM: Round [59] log likelihood: -11794.157008
EM: Round [60] log likelihood: -11794.156892
EM: Round [61] log likelihood: -11794.156782
EM: Round [62] log likelihood: -11794.156679
EM: Round [63] log likelihood: -11794.156582
EM: Stopping iterations at round 63 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9824221 > /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir > /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir --annotate /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir
-done, see /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 104, filtered: 1132)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000234715.2]
WARNING, no entry stored in dbm for [ENSG00000234996.4]
WARNING, no entry stored in dbm for [ENSG00000274712.2]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000280304.1]
WARNING, no entry stored in dbm for [ENSG00000230559.1]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000254743.1]
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WARNING, no entry stored in dbm for [ENSG00000224699.9]
WARNING, no entry stored in dbm for [ENSG00000254034.2]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000225851.1]
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WARNING, no entry stored in dbm for [ENSG00000213409.4]
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WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000286629.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.0jMiK3qXRn/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)