.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (A549_FFPE_01_RNA_0001_B23LG7FLT4_2)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/18cab7a646190160ca611a2a0e1cc0/.command.err
Size: 11.8 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (A549_FFPE_01_RNA_0001_B23LG7FLT4_2)
Attempt
Content

-ctat genome lib [/tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.lUNqPHBMJD/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary
-sample contains 149272 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir  -J /tmp/nxf.lUNqPHBMJD/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction  -O /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.lUNqPHBMJD/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction
-building interval tree based on /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=60000.00/min 
[20000], rate=60000.00/min 
[30000], rate=62068.97/min 
[40000], rate=64864.86/min 
[50000], rate=68181.82/min -building interval tree based on /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=66666.67/min 
[20000], rate=60000.00/min 
[30000], rate=56250.00/min 
[40000], rate=61538.46/min 
[50000], rate=61224.49/min -building interval tree based on /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=54545.45/min 
[20000], rate=54545.45/min 
[30000], rate=50000.00/min 
[40000], rate=52173.91/min 
[50000], rate=55555.56/min -building interval tree based on /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=54545.45/min 
[20000], rate=66666.67/min 
[30000], rate=60000.00/min 
[40000], rate=58536.59/min 
[50000], rate=56603.77/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 6000000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.lUNqPHBMJD/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.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.lUNqPHBMJD/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -1219.612376
EM: Round [1] log likelihood: -1217.733801
EM: Round [2] log likelihood: -1217.106687
EM: Round [3] log likelihood: -1216.841563
EM: Round [4] log likelihood: -1216.712217
EM: Round [5] log likelihood: -1216.642717
EM: Round [6] log likelihood: -1216.602437
EM: Round [7] log likelihood: -1216.577539
EM: Round [8] log likelihood: -1216.561284
EM: Round [9] log likelihood: -1216.550182
EM: Round [10] log likelihood: -1216.542324
EM: Round [11] log likelihood: -1216.536607
EM: Round [12] log likelihood: -1216.532360
EM: Round [13] log likelihood: -1216.529157
EM: Round [14] log likelihood: -1216.526711
EM: Round [15] log likelihood: -1216.524827
EM: Round [16] log likelihood: -1216.523366
EM: Round [17] log likelihood: -1216.522226
EM: Round [18] log likelihood: -1216.521333
EM: Round [19] log likelihood: -1216.520632
EM: Round [20] log likelihood: -1216.520079
EM: Round [21] log likelihood: -1216.519641
EM: Round [22] log likelihood: -1216.519295
EM: Round [23] log likelihood: -1216.519021
EM: Round [24] log likelihood: -1216.518803
EM: Round [25] log likelihood: -1216.518629
EM: Round [26] log likelihood: -1216.518491
EM: Round [27] log likelihood: -1216.518381
EM: Round [28] log likelihood: -1216.518294
EM: Stopping iterations at round 28 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -1219.259027
EM: Round [1] log likelihood: -1217.606122
EM: Round [2] log likelihood: -1217.057506
EM: Round [3] log likelihood: -1216.822176
EM: Round [4] log likelihood: -1216.704508
EM: Round [5] log likelihood: -1216.639640
EM: Round [6] log likelihood: -1216.601207
EM: Round [7] log likelihood: -1216.577048
EM: Round [8] log likelihood: -1216.561088
EM: Round [9] log likelihood: -1216.550104
EM: Round [10] log likelihood: -1216.542292
EM: Round [11] log likelihood: -1216.536594
EM: Round [12] log likelihood: -1216.532355
EM: Round [13] log likelihood: -1216.529155
EM: Round [14] log likelihood: -1216.526710
EM: Round [15] log likelihood: -1216.524827
EM: Round [16] log likelihood: -1216.523366
EM: Round [17] log likelihood: -1216.522226
EM: Round [18] log likelihood: -1216.521333
EM: Round [19] log likelihood: -1216.520632
EM: Round [20] log likelihood: -1216.520079
EM: Round [21] log likelihood: -1216.519641
EM: Round [22] log likelihood: -1216.519295
EM: Round [23] log likelihood: -1216.519021
EM: Round [24] log likelihood: -1216.518803
EM: Round [25] log likelihood: -1216.518629
EM: Round [26] log likelihood: -1216.518491
EM: Round [27] log likelihood: -1216.518381
EM: Round [28] log likelihood: -1216.518294
EM: Stopping iterations at round 28 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 149272 > /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir > /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir --annotate /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir
-done, see /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 15, filtered: 232)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000227195.11]
WARNING, no entry stored in dbm for [ENSG00000257167.2]
WARNING, no entry stored in dbm for [ENSG00000223823.1]
WARNING, no entry stored in dbm for [ENSG00000262151.1]
WARNING, no entry stored in dbm for [ENSG00000223823.1]
WARNING, no entry stored in dbm for [ENSG00000262151.1]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000274021.1]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000228422.5]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000230676.1]
WARNING, no entry stored in dbm for [IGH-.g@-ext]


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