.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-f2a1b0-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/f1a66f0b4c67787665f2b107106ffe/.command.log
Size: 12.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-f2a1b0-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/a7e34c33b2ccabfc7dc5edbcfd6b6e/aih-tih-sc-f2a1b0-R1_A23WJ53LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/ac0898760b67c743e4771421e46995/aih-tih-sc-f2a1b0-R1_A23WJ53LT4_1.Chimeric.out.junction
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/f1a66f0b4c67787665f2b107106ffe/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/a7e34c33b2ccabfc7dc5edbcfd6b6e/aih-tih-sc-f2a1b0-R1_A23WJ53LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/f1a66f0b4c67787665f2b107106ffe/.command.run
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.qdwuEyWs8T/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary
-sample contains 3187237 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir  -J /tmp/nxf.qdwuEyWs8T/aih-tih-sc-f2a1b0-R1_A23WJ53LT4_1.Chimeric.out.junction  -O /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.qdwuEyWs8T/aih-tih-sc-f2a1b0-R1_A23WJ53LT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.qdwuEyWs8T/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=66666.67/min 
[30000], rate=81818.18/min 
[40000], rate=85714.29/min -building interval tree based on /tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=120000.00/min 
[20000], rate=109090.91/min 
[30000], rate=64285.71/min 
[40000], rate=61538.46/min -building interval tree based on /tmp/nxf.qdwuEyWs8T/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=57142.86/min 
[30000], rate=60000.00/min 
[40000], rate=61538.46/min -building interval tree based on /tmp/nxf.qdwuEyWs8T/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=63157.89/min 
[30000], rate=64285.71/min 
[40000], rate=60000.00/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.qdwuEyWs8T/./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.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.qdwuEyWs8T/aih-tih-sc-f2a1b0-R1_A23WJ53LT4_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.qdwuEyWs8T/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -3313.882841
EM: Round [1] log likelihood: -3309.721463
EM: Round [2] log likelihood: -3308.105637
EM: Round [3] log likelihood: -3307.341234
EM: Round [4] log likelihood: -3306.923150
EM: Round [5] log likelihood: -3306.678066
EM: Round [6] log likelihood: -3306.529348
EM: Round [7] log likelihood: -3306.437000
EM: Round [8] log likelihood: -3306.378623
EM: Round [9] log likelihood: -3306.341211
EM: Round [10] log likelihood: -3306.316992
EM: Round [11] log likelihood: -3306.301200
EM: Round [12] log likelihood: -3306.290849
EM: Round [13] log likelihood: -3306.284038
EM: Round [14] log likelihood: -3306.279543
EM: Round [15] log likelihood: -3306.276571
EM: Round [16] log likelihood: -3306.274601
EM: Round [17] log likelihood: -3306.273294
EM: Round [18] log likelihood: -3306.272426
EM: Round [19] log likelihood: -3306.271849
EM: Round [20] log likelihood: -3306.271465
EM: Round [21] log likelihood: -3306.271210
EM: Round [22] log likelihood: -3306.271040
EM: Round [23] log likelihood: -3306.270926
EM: Round [24] log likelihood: -3306.270851
EM: Stopping iterations at round 24 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -3313.659513
EM: Round [1] log likelihood: -3309.593100
EM: Round [2] log likelihood: -3308.030684
EM: Round [3] log likelihood: -3307.297177
EM: Round [4] log likelihood: -3306.896944
EM: Round [5] log likelihood: -3306.662131
EM: Round [6] log likelihood: -3306.519379
EM: Round [7] log likelihood: -3306.430600
EM: Round [8] log likelihood: -3306.374435
EM: Round [9] log likelihood: -3306.338440
EM: Round [10] log likelihood: -3306.315149
EM: Round [11] log likelihood: -3306.299971
EM: Round [12] log likelihood: -3306.290029
EM: Round [13] log likelihood: -3306.283491
EM: Round [14] log likelihood: -3306.279179
EM: Round [15] log likelihood: -3306.276327
EM: Round [16] log likelihood: -3306.274439
EM: Round [17] log likelihood: -3306.273186
EM: Round [18] log likelihood: -3306.272354
EM: Round [19] log likelihood: -3306.271801
EM: Round [20] log likelihood: -3306.271433
EM: Round [21] log likelihood: -3306.271188
EM: Round [22] log likelihood: -3306.271025
EM: Round [23] log likelihood: -3306.270917
EM: Round [24] log likelihood: -3306.270845
EM: Stopping iterations at round 24 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.qdwuEyWs8T/./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.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.qdwuEyWs8T/./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.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 3187237 > /tmp/nxf.qdwuEyWs8T/./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.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir > /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir --annotate /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.qdwuEyWs8T/./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.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir
-done, see /tmp/nxf.qdwuEyWs8T/./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.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.qdwuEyWs8T/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 56, filtered: 658)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.qdwuEyWs8T/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.qdwuEyWs8T/./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.qdwuEyWs8T/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000261420.1]
WARNING, no entry stored in dbm for [ENSG00000225178.5]
WARNING, no entry stored in dbm for [ENSG00000265666.1]
WARNING, no entry stored in dbm for [ENSG00000206975.1]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000250144.1]
WARNING, no entry stored in dbm for [ENSG00000261442.1]
WARNING, no entry stored in dbm for [ENSG00000231528.3]
WARNING, no entry stored in dbm for [ENSG00000254275.6]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000229015.2]
WARNING, no entry stored in dbm for [ENSG00000223478.1]
WARNING, no entry stored in dbm for [ENSG00000279713.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.qdwuEyWs8T/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)