.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (A549_FFPE_01_RNA_0001_B23LG7FLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/da2ebd3ea66f44fa8e6a6b4c81b140/.command.err
Size: 13.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (A549_FFPE_01_RNA_0001_B23LG7FLT4_1)
Attempt
Content

-ctat genome lib [/tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.PqgL0O5dH7/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary
-sample contains 315474 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir  -J /tmp/nxf.PqgL0O5dH7/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.PqgL0O5dH7/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=100000.00/min 
[20000], rate=92307.69/min 
[30000], rate=85714.29/min 
[40000], rate=82758.62/min 
[50000], rate=81081.08/min 
[60000], rate=76595.74/min 
[70000], rate=79245.28/min 
[80000], rate=77419.35/min 
[90000], rate=77142.86/min 
[100000], rate=77922.08/min 
[110000], rate=77647.06/min 
[120000], rate=78260.87/min 
[130000], rate=80412.37/min -building interval tree based on /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=60000.00/min 
[20000], rate=60000.00/min 
[30000], rate=58064.52/min 
[40000], rate=60000.00/min 
[50000], rate=62500.00/min 
[60000], rate=61016.95/min 
[70000], rate=61764.71/min 
[80000], rate=63157.89/min 
[90000], rate=63529.41/min 
[100000], rate=64516.13/min 
[110000], rate=66666.67/min 
[120000], rate=66055.05/min 
[130000], rate=67241.38/min -building interval tree based on /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=50000.00/min 
[20000], rate=63157.89/min 
[30000], rate=69230.77/min 
[40000], rate=68571.43/min 
[50000], rate=69767.44/min 
[60000], rate=69230.77/min 
[70000], rate=70000.00/min 
[80000], rate=69565.22/min 
[90000], rate=71052.63/min 
[100000], rate=70588.24/min 
[110000], rate=67346.94/min 
[120000], rate=63716.81/min 
[130000], rate=63414.63/min -building interval tree based on /tmp/nxf.PqgL0O5dH7/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 
[20000], rate=70588.24/min 
[30000], rate=69230.77/min 
[40000], rate=68571.43/min 
[50000], rate=63829.79/min 
[60000], rate=49315.07/min 
[70000], rate=50000.00/min 
[80000], rate=52747.25/min 
[90000], rate=53465.35/min 
[100000], rate=55045.87/min 
[110000], rate=54098.36/min 
[120000], rate=55384.62/min 
[130000], rate=57352.94/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.PqgL0O5dH7/./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...  
 4500000.00 reads per min processed...  
 4800000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.PqgL0O5dH7/A549_FFPE_01_RNA_0001_B23LG7FLT4_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.PqgL0O5dH7/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -2977.198510
EM: Round [1] log likelihood: -2971.401861
EM: Round [2] log likelihood: -2969.740268
EM: Round [3] log likelihood: -2969.134353
EM: Round [4] log likelihood: -2968.879626
EM: Round [5] log likelihood: -2968.761904
EM: Round [6] log likelihood: -2968.703585
EM: Round [7] log likelihood: -2968.672887
EM: Round [8] log likelihood: -2968.655676
EM: Round [9] log likelihood: -2968.645326
EM: Round [10] log likelihood: -2968.638619
EM: Round [11] log likelihood: -2968.633951
EM: Round [12] log likelihood: -2968.630499
EM: Round [13] log likelihood: -2968.627826
EM: Round [14] log likelihood: -2968.625692
EM: Round [15] log likelihood: -2968.623952
EM: Round [16] log likelihood: -2968.622518
EM: Round [17] log likelihood: -2968.621327
EM: Round [18] log likelihood: -2968.620334
EM: Round [19] log likelihood: -2968.619505
EM: Round [20] log likelihood: -2968.618813
EM: Round [21] log likelihood: -2968.618234
EM: Round [22] log likelihood: -2968.617750
EM: Round [23] log likelihood: -2968.617346
EM: Round [24] log likelihood: -2968.617008
EM: Round [25] log likelihood: -2968.616726
EM: Round [26] log likelihood: -2968.616490
EM: Round [27] log likelihood: -2968.616294
EM: Round [28] log likelihood: -2968.616130
EM: Round [29] log likelihood: -2968.615993
EM: Round [30] log likelihood: -2968.615879
EM: Round [31] log likelihood: -2968.615784
EM: Stopping iterations at round 31 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -2976.975778
EM: Round [1] log likelihood: -2971.288290
EM: Round [2] log likelihood: -2969.682525
EM: Round [3] log likelihood: -2969.105188
EM: Round [4] log likelihood: -2968.864963
EM: Round [5] log likelihood: -2968.754551
EM: Round [6] log likelihood: -2968.699903
EM: Round [7] log likelihood: -2968.671045
EM: Round [8] log likelihood: -2968.654755
EM: Round [9] log likelihood: -2968.644865
EM: Round [10] log likelihood: -2968.638389
EM: Round [11] log likelihood: -2968.633836
EM: Round [12] log likelihood: -2968.630441
EM: Round [13] log likelihood: -2968.627798
EM: Round [14] log likelihood: -2968.625677
EM: Round [15] log likelihood: -2968.623945
EM: Round [16] log likelihood: -2968.622514
EM: Round [17] log likelihood: -2968.621325
EM: Round [18] log likelihood: -2968.620333
EM: Round [19] log likelihood: -2968.619505
EM: Round [20] log likelihood: -2968.618812
EM: Round [21] log likelihood: -2968.618234
EM: Round [22] log likelihood: -2968.617750
EM: Round [23] log likelihood: -2968.617346
EM: Round [24] log likelihood: -2968.617008
EM: Round [25] log likelihood: -2968.616726
EM: Round [26] log likelihood: -2968.616490
EM: Round [27] log likelihood: -2968.616294
EM: Round [28] log likelihood: -2968.616130
EM: Round [29] log likelihood: -2968.615993
EM: Round [30] log likelihood: -2968.615879
EM: Round [31] log likelihood: -2968.615784
EM: Stopping iterations at round 31 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 315474 > /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir > /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir --annotate /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir
-done, see /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 35, filtered: 460)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000279217.1]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000227195.11]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
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WARNING, no entry stored in dbm for [IGH.g@-ext]
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WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000251492.1]
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WARNING, no entry stored in dbm for [ENSG00000230676.1]
WARNING, no entry stored in dbm for [ENSG00000227579.6]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000232628.6]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000205682.2]
WARNING, no entry stored in dbm for [IGL.g@-ext]


	* STAR-Fusion complete.  See output: /tmp/nxf.PqgL0O5dH7/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)