Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/8e08babb03f22aa804f24c05b242aa/659_Kh-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz 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/ef/2d2c0d47249edc3b707731091c5ff8/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/2d2c0d47249edc3b707731091c5ff8/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/9c43bdb841910e432b707a3371459c/659_Kh-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/8e08babb03f22aa804f24c05b242aa/659_Kh-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.R0qlnRCijQ/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary -sample contains 3093294 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir -J /tmp/nxf.R0qlnRCijQ/659_Kh-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction -O /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.R0qlnRCijQ/659_Kh-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=75000.00/min [30000], rate=69230.77/min [40000], rate=68571.43/min -building interval tree based on /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=60000.00/min [30000], rate=62068.97/min [40000], rate=64864.86/min -building interval tree based on /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=63157.89/min [30000], rate=62068.97/min [40000], rate=63157.89/min -building interval tree based on /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=57142.86/min [30000], rate=51428.57/min [40000], rate=53333.33/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir --filt_file /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.R0qlnRCijQ/./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.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.R0qlnRCijQ/659_Kh-T1-TRNA-1_B23MHV2LT4_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.R0qlnRCijQ/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -1744.931859 EM: Round [1] log likelihood: -1744.081095 EM: Round [2] log likelihood: -1743.716098 EM: Round [3] log likelihood: -1743.541503 EM: Round [4] log likelihood: -1743.451948 EM: Round [5] log likelihood: -1743.403561 EM: Round [6] log likelihood: -1743.376321 EM: Round [7] log likelihood: -1743.360466 EM: Round [8] log likelihood: -1743.350983 EM: Round [9] log likelihood: -1743.345182 EM: Round [10] log likelihood: -1743.341567 EM: Round [11] log likelihood: -1743.339281 EM: Round [12] log likelihood: -1743.337818 EM: Round [13] log likelihood: -1743.336873 EM: Round [14] log likelihood: -1743.336258 EM: Round [15] log likelihood: -1743.335855 EM: Round [16] log likelihood: -1743.335591 EM: Round [17] log likelihood: -1743.335416 EM: Round [18] log likelihood: -1743.335301 EM: Round [19] log likelihood: -1743.335224 EM: Stopping iterations at round 19 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.R0qlnRCijQ/./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.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.R0qlnRCijQ/./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.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 3093294 > /tmp/nxf.R0qlnRCijQ/./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.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir > /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir --annotate /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.R0qlnRCijQ/./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.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir -done, see /tmp/nxf.R0qlnRCijQ/./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.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.R0qlnRCijQ/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 67, filtered: 267) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.R0qlnRCijQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.R0qlnRCijQ/./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.R0qlnRCijQ/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000228463.10] 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 [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000260239.2] WARNING, no entry stored in dbm for [ENSG00000239572.3] WARNING, no entry stored in dbm for [ENSG00000281131.1] WARNING, no entry stored in dbm for [ENSG00000227070.1] 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 [ENSG00000217488.2] WARNING, no entry stored in dbm for [ENSG00000237491.10] WARNING, no entry stored in dbm for [ENSG00000281912.1] WARNING, no entry stored in dbm for [ENSG00000241469.9] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000230894.2] 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 [ENSG00000254092.2] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000254092.2] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000237294.1] 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 [ENSG00000231367.6] WARNING, no entry stored in dbm for [ENSG00000229930.1] WARNING, no entry stored in dbm for [ENSG00000272693.4] WARNING, no entry stored in dbm for [ENSG00000254260.1] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000254260.1] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000230305.2] * STAR-Fusion complete. See output: /tmp/nxf.R0qlnRCijQ/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)