.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (rna_s1221_S42)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/4aa4cd953b9a2ed024f6836009009f/.command.err
Size: 19.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (rna_s1221_S42)
Attempt
Content

-ctat genome lib [/tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.bIyAQW6hB4/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary
-sample contains 9932006 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir  -J /tmp/nxf.bIyAQW6hB4/rna_s1221_S42.Chimeric.out.junction  -O /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.bIyAQW6hB4/rna_s1221_S42.Chimeric.out.junction
-building interval tree based on /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=150000.00/min 
[20000], rate=240000.00/min 
[30000], rate=360000.00/min 
[40000], rate=400000.00/min 
[50000], rate=375000.00/min 
[60000], rate=276923.08/min 
[70000], rate=247058.82/min 
[80000], rate=228571.43/min 
[90000], rate=216000.00/min 
[100000], rate=240000.00/min 
[110000], rate=253846.15/min 
[120000], rate=276923.08/min 
[130000], rate=268965.52/min 
[140000], rate=270967.74/min -building interval tree based on /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=100000.00/min 
[20000], rate=171428.57/min 
[30000], rate=180000.00/min 
[40000], rate=150000.00/min 
[50000], rate=176470.59/min 
[60000], rate=180000.00/min 
[70000], rate=168000.00/min 
[80000], rate=177777.78/min 
[90000], rate=168750.00/min 
[100000], rate=162162.16/min 
[110000], rate=173684.21/min 
[120000], rate=146938.78/min 
[130000], rate=123809.52/min -building interval tree based on /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=100000.00/min 
[20000], rate=133333.33/min 
[30000], rate=128571.43/min 
[40000], rate=120000.00/min 
[50000], rate=100000.00/min 
[60000], rate=97297.30/min 
[70000], rate=93333.33/min 
[80000], rate=92307.69/min 
[90000], rate=88524.59/min 
[100000], rate=88235.29/min 
[110000], rate=88000.00/min 
[120000], rate=87804.88/min 
[130000], rate=89655.17/min -building interval tree based on /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=100000.00/min 
[20000], rate=75000.00/min 
[30000], rate=69230.77/min 
[40000], rate=75000.00/min 
[50000], rate=78947.37/min 
[60000], rate=80000.00/min 
[70000], rate=77777.78/min 
[80000], rate=77419.35/min 
[90000], rate=76056.34/min 
[100000], rate=77922.08/min 
[110000], rate=75862.07/min 
[120000], rate=74226.80/min 
[130000], rate=75000.00/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 6000000.00 reads per min processed...  
 4000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.bIyAQW6hB4/rna_s1221_S42.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.bIyAQW6hB4/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -23093.648792
EM: Round [1] log likelihood: -23087.484357
EM: Round [2] log likelihood: -23085.050891
EM: Round [3] log likelihood: -23083.773025
EM: Round [4] log likelihood: -23083.019702
EM: Round [5] log likelihood: -23082.544715
EM: Round [6] log likelihood: -23082.228764
EM: Round [7] log likelihood: -23082.008530
EM: Round [8] log likelihood: -23081.848638
EM: Round [9] log likelihood: -23081.728487
EM: Round [10] log likelihood: -23081.635597
EM: Round [11] log likelihood: -23081.562112
EM: Round [12] log likelihood: -23081.502898
EM: Round [13] log likelihood: -23081.454481
EM: Round [14] log likelihood: -23081.414427
EM: Round [15] log likelihood: -23081.380982
EM: Round [16] log likelihood: -23081.352846
EM: Round [17] log likelihood: -23081.329033
EM: Round [18] log likelihood: -23081.308779
EM: Round [19] log likelihood: -23081.291483
EM: Round [20] log likelihood: -23081.276662
EM: Round [21] log likelihood: -23081.263928
EM: Round [22] log likelihood: -23081.252960
EM: Round [23] log likelihood: -23081.243496
EM: Round [24] log likelihood: -23081.235316
EM: Round [25] log likelihood: -23081.228234
EM: Round [26] log likelihood: -23081.222097
EM: Round [27] log likelihood: -23081.216772
EM: Round [28] log likelihood: -23081.212149
EM: Round [29] log likelihood: -23081.208131
EM: Round [30] log likelihood: -23081.204636
EM: Round [31] log likelihood: -23081.201596
EM: Round [32] log likelihood: -23081.198949
EM: Round [33] log likelihood: -23081.196643
EM: Round [34] log likelihood: -23081.194634
EM: Round [35] log likelihood: -23081.192882
EM: Round [36] log likelihood: -23081.191355
EM: Round [37] log likelihood: -23081.190023
EM: Round [38] log likelihood: -23081.188861
EM: Round [39] log likelihood: -23081.187848
EM: Round [40] log likelihood: -23081.186963
EM: Round [41] log likelihood: -23081.186190
EM: Round [42] log likelihood: -23081.185516
EM: Round [43] log likelihood: -23081.184927
EM: Round [44] log likelihood: -23081.184412
EM: Round [45] log likelihood: -23081.183963
EM: Round [46] log likelihood: -23081.183571
EM: Round [47] log likelihood: -23081.183228
EM: Round [48] log likelihood: -23081.182928
EM: Round [49] log likelihood: -23081.182667
EM: Round [50] log likelihood: -23081.182438
EM: Round [51] log likelihood: -23081.182238
EM: Round [52] log likelihood: -23081.182064
EM: Round [53] log likelihood: -23081.181911
EM: Round [54] log likelihood: -23081.181778
EM: Round [55] log likelihood: -23081.181661
EM: Round [56] log likelihood: -23081.181559
EM: Round [57] log likelihood: -23081.181470
EM: Stopping iterations at round 57 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -23092.947677
EM: Round [1] log likelihood: -23087.121344
EM: Round [2] log likelihood: -23084.825823
EM: Round [3] log likelihood: -23083.616951
EM: Round [4] log likelihood: -23082.904429
EM: Round [5] log likelihood: -23082.456701
EM: Round [6] log likelihood: -23082.160382
EM: Round [7] log likelihood: -23081.954893
EM: Round [8] log likelihood: -23081.806331
EM: Round [9] log likelihood: -23081.694997
EM: Round [10] log likelihood: -23081.609021
EM: Round [11] log likelihood: -23081.540985
EM: Round [12] log likelihood: -23081.486081
EM: Round [13] log likelihood: -23081.441080
EM: Round [14] log likelihood: -23081.403740
EM: Round [15] log likelihood: -23081.372453
EM: Round [16] log likelihood: -23081.346037
EM: Round [17] log likelihood: -23081.323594
EM: Round [18] log likelihood: -23081.304434
EM: Round [19] log likelihood: -23081.288010
EM: Round [20] log likelihood: -23081.273886
EM: Round [21] log likelihood: -23081.261708
EM: Round [22] log likelihood: -23081.251186
EM: Round [23] log likelihood: -23081.242077
EM: Round [24] log likelihood: -23081.234181
EM: Round [25] log likelihood: -23081.227327
EM: Round [26] log likelihood: -23081.221371
EM: Round [27] log likelihood: -23081.216192
EM: Round [28] log likelihood: -23081.211684
EM: Round [29] log likelihood: -23081.207759
EM: Round [30] log likelihood: -23081.204339
EM: Round [31] log likelihood: -23081.201358
EM: Round [32] log likelihood: -23081.198758
EM: Round [33] log likelihood: -23081.196491
EM: Round [34] log likelihood: -23081.194512
EM: Round [35] log likelihood: -23081.192785
EM: Round [36] log likelihood: -23081.191277
EM: Round [37] log likelihood: -23081.189961
EM: Round [38] log likelihood: -23081.188812
EM: Round [39] log likelihood: -23081.187808
EM: Round [40] log likelihood: -23081.186931
EM: Round [41] log likelihood: -23081.186165
EM: Round [42] log likelihood: -23081.185495
EM: Round [43] log likelihood: -23081.184910
EM: Round [44] log likelihood: -23081.184399
EM: Round [45] log likelihood: -23081.183953
EM: Round [46] log likelihood: -23081.183562
EM: Round [47] log likelihood: -23081.183221
EM: Round [48] log likelihood: -23081.182923
EM: Round [49] log likelihood: -23081.182662
EM: Round [50] log likelihood: -23081.182435
EM: Round [51] log likelihood: -23081.182236
EM: Round [52] log likelihood: -23081.182061
EM: Round [53] log likelihood: -23081.181909
EM: Round [54] log likelihood: -23081.181776
EM: Round [55] log likelihood: -23081.181660
EM: Round [56] log likelihood: -23081.181558
EM: Round [57] log likelihood: -23081.181469
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.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.bIyAQW6hB4/./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.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.bIyAQW6hB4/./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.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9932006 > /tmp/nxf.bIyAQW6hB4/./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.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir > /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir --annotate /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.bIyAQW6hB4/./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.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir
-done, see /tmp/nxf.bIyAQW6hB4/./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.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.bIyAQW6hB4/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 452, filtered: 1791)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.bIyAQW6hB4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.bIyAQW6hB4/./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.bIyAQW6hB4/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000180747.15]
WARNING, no entry stored in dbm for [ENSG00000205534.6]
WARNING, no entry stored in dbm for [ENSG00000254485.5]
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WARNING, no entry stored in dbm for [ENSG00000232894.1]
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WARNING, no entry stored in dbm for [ENSG00000243004.6]
WARNING, no entry stored in dbm for [ENSG00000265206.5]
WARNING, no entry stored in dbm for [ENSG00000237296.9]


	* STAR-Fusion complete.  See output: /tmp/nxf.bIyAQW6hB4/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)