.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/a7f3e07c3c224e166d137e41d57cc2/.command.err
Size: 13.6 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt
Content

-ctat genome lib [/tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.ApftGg0uOS/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary
-sample contains 4362646 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir  -J /tmp/nxf.ApftGg0uOS/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction  -O /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.ApftGg0uOS/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=42857.14/min 
[20000], rate=44444.44/min 
[30000], rate=50000.00/min 
[40000], rate=52173.91/min 
[50000], rate=50847.46/min -building interval tree based on /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=85714.29/min 
[20000], rate=54545.45/min 
[30000], rate=51428.57/min 
[40000], rate=51063.83/min 
[50000], rate=50847.46/min -building interval tree based on /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=50000.00/min 
[20000], rate=50000.00/min 
[30000], rate=47368.42/min 
[40000], rate=47058.82/min 
[50000], rate=46875.00/min -building interval tree based on /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=66666.67/min 
[20000], rate=57142.86/min 
[30000], rate=46153.85/min 
[40000], rate=43636.36/min 
[50000], rate=44117.65/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.ApftGg0uOS/1173_OHF_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.ApftGg0uOS/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -9780.615024
EM: Round [1] log likelihood: -9775.588806
EM: Round [2] log likelihood: -9773.274349
EM: Round [3] log likelihood: -9772.070101
EM: Round [4] log likelihood: -9771.412894
EM: Round [5] log likelihood: -9771.043899
EM: Round [6] log likelihood: -9770.831238
EM: Round [7] log likelihood: -9770.705320
EM: Round [8] log likelihood: -9770.628774
EM: Round [9] log likelihood: -9770.581119
EM: Round [10] log likelihood: -9770.550836
EM: Round [11] log likelihood: -9770.531262
EM: Round [12] log likelihood: -9770.518433
EM: Round [13] log likelihood: -9770.509926
EM: Round [14] log likelihood: -9770.504233
EM: Round [15] log likelihood: -9770.500392
EM: Round [16] log likelihood: -9770.497784
EM: Round [17] log likelihood: -9770.496002
EM: Round [18] log likelihood: -9770.494778
EM: Round [19] log likelihood: -9770.493934
EM: Round [20] log likelihood: -9770.493349
EM: Round [21] log likelihood: -9770.492942
EM: Round [22] log likelihood: -9770.492657
EM: Round [23] log likelihood: -9770.492458
EM: Round [24] log likelihood: -9770.492317
EM: Round [25] log likelihood: -9770.492218
EM: Stopping iterations at round 25 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -9780.209559
EM: Round [1] log likelihood: -9775.406485
EM: Round [2] log likelihood: -9773.187337
EM: Round [3] log likelihood: -9772.027541
EM: Round [4] log likelihood: -9771.391840
EM: Round [5] log likelihood: -9771.033428
EM: Round [6] log likelihood: -9770.826016
EM: Round [7] log likelihood: -9770.702713
EM: Round [8] log likelihood: -9770.627471
EM: Round [9] log likelihood: -9770.580468
EM: Round [10] log likelihood: -9770.550511
EM: Round [11] log likelihood: -9770.531100
EM: Round [12] log likelihood: -9770.518351
EM: Round [13] log likelihood: -9770.509886
EM: Round [14] log likelihood: -9770.504213
EM: Round [15] log likelihood: -9770.500382
EM: Round [16] log likelihood: -9770.497779
EM: Round [17] log likelihood: -9770.496000
EM: Round [18] log likelihood: -9770.494777
EM: Round [19] log likelihood: -9770.493934
EM: Round [20] log likelihood: -9770.493349
EM: Round [21] log likelihood: -9770.492942
EM: Round [22] log likelihood: -9770.492657
EM: Round [23] log likelihood: -9770.492458
EM: Round [24] log likelihood: -9770.492317
EM: Round [25] log likelihood: -9770.492218
EM: Stopping iterations at round 25 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 4362646 > /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir > /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir --annotate /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir
-done, see /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 190, filtered: 1157)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
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	* STAR-Fusion complete.  See output: /tmp/nxf.ApftGg0uOS/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)