.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/70/e6b559700dc9411e505b1a89de2cae/.command.err
Size: 17.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (rna_s1221_S42)
Attempt
Content

-ctat genome lib [/tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.DJxdw9QeuC/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary
-sample contains 9928008 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir  -J /tmp/nxf.DJxdw9QeuC/rna_s1221_S42.Chimeric.out.junction  -O /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.DJxdw9QeuC/rna_s1221_S42.Chimeric.out.junction
-building interval tree based on /tmp/nxf.DJxdw9QeuC/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=300000.00/min 
[30000], rate=360000.00/min 
[40000], rate=480000.00/min 
[50000], rate=375000.00/min 
[60000], rate=240000.00/min 
[70000], rate=200000.00/min 
[80000], rate=184615.38/min 
[90000], rate=192857.14/min 
[100000], rate=206896.55/min 
[110000], rate=227586.21/min 
[120000], rate=240000.00/min 
[130000], rate=229411.76/min -building interval tree based on /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes

[10000], rate=100000.00/min 
[20000], rate=150000.00/min 
[30000], rate=180000.00/min 
[40000], rate=150000.00/min 
[50000], rate=176470.59/min 
[60000], rate=180000.00/min 
[70000], rate=161538.46/min 
[80000], rate=171428.57/min 
[90000], rate=168750.00/min 
[100000], rate=162162.16/min 
[110000], rate=165000.00/min 
[120000], rate=138461.54/min 
[130000], rate=121875.00/min -building interval tree based on /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes

[10000], rate=100000.00/min 
[20000], rate=120000.00/min 
[30000], rate=120000.00/min 
[40000], rate=100000.00/min 
[50000], rate=88235.29/min 
[60000], rate=87804.88/min 
[70000], rate=85714.29/min 
[80000], rate=84210.53/min 
[90000], rate=83076.92/min 
[100000], rate=82191.78/min 
[110000], rate=82500.00/min 
[120000], rate=82758.62/min 
[130000], rate=83870.97/min -building interval tree based on /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes

[10000], rate=85714.29/min 
[20000], rate=57142.86/min 
[30000], rate=52941.18/min 
[40000], rate=57142.86/min 
[50000], rate=62500.00/min 
[60000], rate=64285.71/min 
[70000], rate=64615.38/min 
[80000], rate=64864.86/min 
[90000], rate=65853.66/min 
[100000], rate=66666.67/min 
[110000], rate=66666.67/min 
[120000], rate=65454.55/min 
[130000], rate=66666.67/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.DJxdw9QeuC/./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.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.DJxdw9QeuC/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.DJxdw9QeuC/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -22282.609139
EM: Round [1] log likelihood: -22275.314643
EM: Round [2] log likelihood: -22272.586423
EM: Round [3] log likelihood: -22271.361773
EM: Round [4] log likelihood: -22270.737261
EM: Round [5] log likelihood: -22270.388454
EM: Round [6] log likelihood: -22270.180025
EM: Round [7] log likelihood: -22270.048580
EM: Round [8] log likelihood: -22269.961851
EM: Round [9] log likelihood: -22269.902398
EM: Round [10] log likelihood: -22269.860331
EM: Round [11] log likelihood: -22269.829794
EM: Round [12] log likelihood: -22269.807177
EM: Round [13] log likelihood: -22269.790163
EM: Round [14] log likelihood: -22269.777210
EM: Round [15] log likelihood: -22269.767261
EM: Round [16] log likelihood: -22269.759565
EM: Round [17] log likelihood: -22269.753582
EM: Round [18] log likelihood: -22269.748910
EM: Round [19] log likelihood: -22269.745250
EM: Round [20] log likelihood: -22269.742377
EM: Round [21] log likelihood: -22269.740115
EM: Round [22] log likelihood: -22269.738332
EM: Round [23] log likelihood: -22269.736925
EM: Round [24] log likelihood: -22269.735813
EM: Round [25] log likelihood: -22269.734933
EM: Round [26] log likelihood: -22269.734236
EM: Round [27] log likelihood: -22269.733683
EM: Round [28] log likelihood: -22269.733245
EM: Round [29] log likelihood: -22269.732898
EM: Round [30] log likelihood: -22269.732621
EM: Round [31] log likelihood: -22269.732402
EM: Round [32] log likelihood: -22269.732228
EM: Round [33] log likelihood: -22269.732089
EM: Round [34] log likelihood: -22269.731979
EM: Round [35] log likelihood: -22269.731891
EM: Stopping iterations at round 35 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -22282.433542
EM: Round [1] log likelihood: -22275.263238
EM: Round [2] log likelihood: -22272.570720
EM: Round [3] log likelihood: -22271.357516
EM: Round [4] log likelihood: -22270.736685
EM: Round [5] log likelihood: -22270.388945
EM: Round [6] log likelihood: -22270.180709
EM: Round [7] log likelihood: -22270.049188
EM: Round [8] log likelihood: -22269.962324
EM: Round [9] log likelihood: -22269.902745
EM: Round [10] log likelihood: -22269.860577
EM: Round [11] log likelihood: -22269.829965
EM: Round [12] log likelihood: -22269.807294
EM: Round [13] log likelihood: -22269.790243
EM: Round [14] log likelihood: -22269.777265
EM: Round [15] log likelihood: -22269.767298
EM: Round [16] log likelihood: -22269.759590
EM: Round [17] log likelihood: -22269.753598
EM: Round [18] log likelihood: -22269.748921
EM: Round [19] log likelihood: -22269.745258
EM: Round [20] log likelihood: -22269.742382
EM: Round [21] log likelihood: -22269.740118
EM: Round [22] log likelihood: -22269.738335
EM: Round [23] log likelihood: -22269.736927
EM: Round [24] log likelihood: -22269.735814
EM: Round [25] log likelihood: -22269.734933
EM: Round [26] log likelihood: -22269.734236
EM: Round [27] log likelihood: -22269.733684
EM: Round [28] log likelihood: -22269.733245
EM: Round [29] log likelihood: -22269.732898
EM: Round [30] log likelihood: -22269.732622
EM: Round [31] log likelihood: -22269.732402
EM: Round [32] log likelihood: -22269.732228
EM: Round [33] log likelihood: -22269.732089
EM: Round [34] log likelihood: -22269.731979
EM: Round [35] log likelihood: -22269.731891
EM: Stopping iterations at round 35 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.DJxdw9QeuC/./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.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.DJxdw9QeuC/./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.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9928008 > /tmp/nxf.DJxdw9QeuC/./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.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir > /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir --annotate /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.DJxdw9QeuC/./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.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir
-done, see /tmp/nxf.DJxdw9QeuC/./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.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.DJxdw9QeuC/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 450, filtered: 1748)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.DJxdw9QeuC/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.DJxdw9QeuC/./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.DJxdw9QeuC/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000282458.1]
WARNING, no entry stored in dbm for [ENSG00000278903.3]
WARNING, no entry stored in dbm for [ENSG00000111788.10]
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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 [ENSG00000189149.12]
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WARNING, no entry stored in dbm for [ENSG00000269968.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.DJxdw9QeuC/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)