.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/bded76a6f47e1fc5b1257f5cf09942/.command.err
Size: 22.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt
Content

-ctat genome lib [/tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.OXh4JSv4Hu/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary
-sample contains 15421621 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir  -J /tmp/nxf.OXh4JSv4Hu/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction  -O /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.OXh4JSv4Hu/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes

[10000], rate=50000.00/min 
[20000], rate=50000.00/min 
[30000], rate=46153.85/min 
[40000], rate=47058.82/min 
[50000], rate=49180.33/min 
[60000], rate=48648.65/min 
[70000], rate=48837.21/min 
[80000], rate=48979.59/min 
[90000], rate=48648.65/min 
[100000], rate=48780.49/min 
[110000], rate=48888.89/min 
[120000], rate=49655.17/min 
[130000], rate=50000.00/min 
[140000], rate=50602.41/min 
[150000], rate=51136.36/min -building interval tree based on /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes

[10000], rate=33333.33/min 
[20000], rate=38709.68/min 
[30000], rate=41860.47/min 
[40000], rate=38095.24/min 
[50000], rate=37974.68/min 
[60000], rate=39560.44/min 
[70000], rate=41584.16/min 
[80000], rate=43243.24/min 
[90000], rate=45000.00/min 
[100000], rate=46511.63/min 
[110000], rate=47826.09/min 
[120000], rate=49315.07/min 
[130000], rate=50000.00/min 
[140000], rate=49411.76/min 
[150000], rate=49180.33/min -building interval tree based on /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=33333.33/min 
[20000], rate=40000.00/min 
[30000], rate=46153.85/min 
[40000], rate=46153.85/min 
[50000], rate=50000.00/min 
[60000], rate=50704.23/min 
[70000], rate=52500.00/min 
[80000], rate=50526.32/min 
[90000], rate=49541.28/min 
[100000], rate=49180.33/min 
[110000], rate=49253.73/min 
[120000], rate=48322.15/min 
[130000], rate=48148.15/min 
[140000], rate=47457.63/min 
[150000], rate=47368.42/min -building interval tree based on /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes

[10000], rate=66666.67/min 
[20000], rate=66666.67/min 
[30000], rate=75000.00/min 
[40000], rate=61538.46/min 
[50000], rate=48387.10/min 
[60000], rate=45000.00/min 
[70000], rate=44210.53/min 
[80000], rate=44859.81/min 
[90000], rate=45378.15/min 
[100000], rate=45801.53/min 
[110000], rate=45833.33/min 
[120000], rate=45283.02/min 
[130000], rate=44318.18/min 
[140000], rate=43298.97/min 
[150000], rate=43062.20/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 3000000.00 reads per min processed...  
 2000000.00 reads per min processed...  
 2250000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.OXh4JSv4Hu/1173_GZ1_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.OXh4JSv4Hu/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -104324.186898
EM: Round [1] log likelihood: -104310.356843
EM: Round [2] log likelihood: -104305.900718
EM: Round [3] log likelihood: -104303.894569
EM: Round [4] log likelihood: -104302.846703
EM: Round [5] log likelihood: -104302.253728
EM: Round [6] log likelihood: -104301.900038
EM: Round [7] log likelihood: -104301.680766
EM: Round [8] log likelihood: -104301.540704
EM: Round [9] log likelihood: -104301.449082
EM: Round [10] log likelihood: -104301.387979
EM: Round [11] log likelihood: -104301.346579
EM: Round [12] log likelihood: -104301.318157
EM: Round [13] log likelihood: -104301.298428
EM: Round [14] log likelihood: -104301.284605
EM: Round [15] log likelihood: -104301.274842
EM: Round [16] log likelihood: -104301.267899
EM: Round [17] log likelihood: -104301.262931
EM: Round [18] log likelihood: -104301.259358
EM: Round [19] log likelihood: -104301.256776
EM: Round [20] log likelihood: -104301.254903
EM: Round [21] log likelihood: -104301.253539
EM: Round [22] log likelihood: -104301.252542
EM: Round [23] log likelihood: -104301.251812
EM: Round [24] log likelihood: -104301.251276
EM: Round [25] log likelihood: -104301.250881
EM: Round [26] log likelihood: -104301.250589
EM: Round [27] log likelihood: -104301.250374
EM: Round [28] log likelihood: -104301.250214
EM: Round [29] log likelihood: -104301.250096
EM: Round [30] log likelihood: -104301.250008
EM: Stopping iterations at round 30 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -104277.978360
EM: Round [1] log likelihood: -104267.571178
EM: Round [2] log likelihood: -104263.924912
EM: Round [3] log likelihood: -104262.209072
EM: Round [4] log likelihood: -104261.297032
EM: Round [5] log likelihood: -104260.779053
EM: Round [6] log likelihood: -104260.471270
EM: Round [7] log likelihood: -104260.282025
EM: Round [8] log likelihood: -104260.162481
EM: Round [9] log likelihood: -104260.085298
EM: Round [10] log likelihood: -104260.034562
EM: Round [11] log likelihood: -104260.000705
EM: Round [12] log likelihood: -104259.977823
EM: Round [13] log likelihood: -104259.962189
EM: Round [14] log likelihood: -104259.951407
EM: Round [15] log likelihood: -104259.943908
EM: Round [16] log likelihood: -104259.938655
EM: Round [17] log likelihood: -104259.934951
EM: Round [18] log likelihood: -104259.932323
EM: Round [19] log likelihood: -104259.930449
EM: Round [20] log likelihood: -104259.929106
EM: Round [21] log likelihood: -104259.928139
EM: Round [22] log likelihood: -104259.927440
EM: Round [23] log likelihood: -104259.926933
EM: Round [24] log likelihood: -104259.926564
EM: Round [25] log likelihood: -104259.926294
EM: Round [26] log likelihood: -104259.926097
EM: Round [27] log likelihood: -104259.925952
EM: Round [28] log likelihood: -104259.925846
EM: Round [29] log likelihood: -104259.925767
EM: Stopping iterations at round 29 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.OXh4JSv4Hu/./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.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.OXh4JSv4Hu/./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.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 15421621 > /tmp/nxf.OXh4JSv4Hu/./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.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir > /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir --annotate /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.OXh4JSv4Hu/./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.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir
-done, see /tmp/nxf.OXh4JSv4Hu/./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.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.OXh4JSv4Hu/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 743, filtered: 5671)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.OXh4JSv4Hu/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.OXh4JSv4Hu/./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.OXh4JSv4Hu/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGH.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000259577.2]
WARNING, no entry stored in dbm for [ENSG00000273192.1]
WARNING, no entry stored in dbm for [ENSG00000230021.10]
WARNING, no entry stored in dbm for [ENSG00000230021.10]
WARNING, no entry stored in dbm for [ENSG00000232499.2]
WARNING, no entry stored in dbm for [ENSG00000226647.2]
WARNING, no entry stored in dbm for [ENSG00000247970.2]
WARNING, no entry stored in dbm for [ENSG00000259137.1]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000274760.1]
WARNING, no entry stored in dbm for [ENSG00000279833.1]
WARNING, no entry stored in dbm for [ENSG00000279833.1]
WARNING, no entry stored in dbm for [ENSG00000279123.1]
WARNING, no entry stored in dbm for [ENSG00000279080.1]
WARNING, no entry stored in dbm for [ENSG00000237476.1]
WARNING, no entry stored in dbm for [ENSG00000261143.1]
WARNING, no entry stored in dbm for [ENSG00000244101.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000286830.1]
WARNING, no entry stored in dbm for [ENSG00000257398.8]
WARNING, no entry stored in dbm for [ENSG00000219410.6]
WARNING, no entry stored in dbm for [ENSG00000262979.1]
WARNING, no entry stored in dbm for [ENSG00000250159.7]
WARNING, no entry stored in dbm for [ENSG00000236942.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000276538.1]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000285331.2]
WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000249685.1]
WARNING, no entry stored in dbm for [ENSG00000283674.3]
WARNING, no entry stored in dbm for [ENSG00000267102.1]
WARNING, no entry stored in dbm for [ENSG00000254485.5]
WARNING, no entry stored in dbm for [ENSG00000238045.9]
WARNING, no entry stored in dbm for [ENSG00000284649.1]
WARNING, no entry stored in dbm for [ENSG00000214331.8]
WARNING, no entry stored in dbm for [ENSG00000257403.2]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000287603.1]
WARNING, no entry stored in dbm for [ENSG00000284052.1]
WARNING, no entry stored in dbm for [ENSG00000205485.13]


	* STAR-Fusion complete.  See output: /tmp/nxf.OXh4JSv4Hu/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)