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/3e/da2ebd3ea66f44fa8e6a6b4c81b140/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/da2ebd3ea66f44fa8e6a6b4c81b140/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/12f2a9751cbef520fa84fd1bf1e414/A549_FFPE_01_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/12f2a9751cbef520fa84fd1bf1e414/A549_FFPE_01_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/1832b6439c06db8f647edc539c8772/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.PqgL0O5dH7/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary -sample contains 315474 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir -J /tmp/nxf.PqgL0O5dH7/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.PqgL0O5dH7/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=92307.69/min [30000], rate=85714.29/min [40000], rate=82758.62/min [50000], rate=81081.08/min [60000], rate=76595.74/min [70000], rate=79245.28/min [80000], rate=77419.35/min [90000], rate=77142.86/min [100000], rate=77922.08/min [110000], rate=77647.06/min [120000], rate=78260.87/min [130000], rate=80412.37/min -building interval tree based on /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=60000.00/min [20000], rate=60000.00/min [30000], rate=58064.52/min [40000], rate=60000.00/min [50000], rate=62500.00/min [60000], rate=61016.95/min [70000], rate=61764.71/min [80000], rate=63157.89/min [90000], rate=63529.41/min [100000], rate=64516.13/min [110000], rate=66666.67/min [120000], rate=66055.05/min [130000], rate=67241.38/min -building interval tree based on /tmp/nxf.PqgL0O5dH7/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=63157.89/min [30000], rate=69230.77/min [40000], rate=68571.43/min [50000], rate=69767.44/min [60000], rate=69230.77/min [70000], rate=70000.00/min [80000], rate=69565.22/min [90000], rate=71052.63/min [100000], rate=70588.24/min [110000], rate=67346.94/min [120000], rate=63716.81/min [130000], rate=63414.63/min -building interval tree based on /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=70588.24/min [30000], rate=69230.77/min [40000], rate=68571.43/min [50000], rate=63829.79/min [60000], rate=49315.07/min [70000], rate=50000.00/min [80000], rate=52747.25/min [90000], rate=53465.35/min [100000], rate=55045.87/min [110000], rate=54098.36/min [120000], rate=55384.62/min [130000], rate=57352.94/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir --filt_file /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.PqgL0O5dH7/./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... 4500000.00 reads per min processed... 4800000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.PqgL0O5dH7/A549_FFPE_01_RNA_0001_B23LG7FLT4_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.PqgL0O5dH7/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -2977.198510 EM: Round [1] log likelihood: -2971.401861 EM: Round [2] log likelihood: -2969.740268 EM: Round [3] log likelihood: -2969.134353 EM: Round [4] log likelihood: -2968.879626 EM: Round [5] log likelihood: -2968.761904 EM: Round [6] log likelihood: -2968.703585 EM: Round [7] log likelihood: -2968.672887 EM: Round [8] log likelihood: -2968.655676 EM: Round [9] log likelihood: -2968.645326 EM: Round [10] log likelihood: -2968.638619 EM: Round [11] log likelihood: -2968.633951 EM: Round [12] log likelihood: -2968.630499 EM: Round [13] log likelihood: -2968.627826 EM: Round [14] log likelihood: -2968.625692 EM: Round [15] log likelihood: -2968.623952 EM: Round [16] log likelihood: -2968.622518 EM: Round [17] log likelihood: -2968.621327 EM: Round [18] log likelihood: -2968.620334 EM: Round [19] log likelihood: -2968.619505 EM: Round [20] log likelihood: -2968.618813 EM: Round [21] log likelihood: -2968.618234 EM: Round [22] log likelihood: -2968.617750 EM: Round [23] log likelihood: -2968.617346 EM: Round [24] log likelihood: -2968.617008 EM: Round [25] log likelihood: -2968.616726 EM: Round [26] log likelihood: -2968.616490 EM: Round [27] log likelihood: -2968.616294 EM: Round [28] log likelihood: -2968.616130 EM: Round [29] log likelihood: -2968.615993 EM: Round [30] log likelihood: -2968.615879 EM: Round [31] log likelihood: -2968.615784 EM: Stopping iterations at round 31 due to insufficient improvement in likelihood. EM: Starting log likelihood: -2976.975778 EM: Round [1] log likelihood: -2971.288290 EM: Round [2] log likelihood: -2969.682525 EM: Round [3] log likelihood: -2969.105188 EM: Round [4] log likelihood: -2968.864963 EM: Round [5] log likelihood: -2968.754551 EM: Round [6] log likelihood: -2968.699903 EM: Round [7] log likelihood: -2968.671045 EM: Round [8] log likelihood: -2968.654755 EM: Round [9] log likelihood: -2968.644865 EM: Round [10] log likelihood: -2968.638389 EM: Round [11] log likelihood: -2968.633836 EM: Round [12] log likelihood: -2968.630441 EM: Round [13] log likelihood: -2968.627798 EM: Round [14] log likelihood: -2968.625677 EM: Round [15] log likelihood: -2968.623945 EM: Round [16] log likelihood: -2968.622514 EM: Round [17] log likelihood: -2968.621325 EM: Round [18] log likelihood: -2968.620333 EM: Round [19] log likelihood: -2968.619505 EM: Round [20] log likelihood: -2968.618812 EM: Round [21] log likelihood: -2968.618234 EM: Round [22] log likelihood: -2968.617750 EM: Round [23] log likelihood: -2968.617346 EM: Round [24] log likelihood: -2968.617008 EM: Round [25] log likelihood: -2968.616726 EM: Round [26] log likelihood: -2968.616490 EM: Round [27] log likelihood: -2968.616294 EM: Round [28] log likelihood: -2968.616130 EM: Round [29] log likelihood: -2968.615993 EM: Round [30] log likelihood: -2968.615879 EM: Round [31] log likelihood: -2968.615784 EM: Stopping iterations at round 31 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 315474 > /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir > /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir --annotate /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir -done, see /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.PqgL0O5dH7/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 35, filtered: 460) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.PqgL0O5dH7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.PqgL0O5dH7/./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.PqgL0O5dH7/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000279217.1] 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 [ENSG00000224255.2] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] 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 [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.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 [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 [ENSG00000228422.5] 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 [ENSG00000251492.1] WARNING, no entry stored in dbm for [ENSG00000260807.7] WARNING, no entry stored in dbm for [ENSG00000230676.1] WARNING, no entry stored in dbm for [ENSG00000227579.6] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000227579.6] 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 [ENSG00000232628.6] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000205682.2] WARNING, no entry stored in dbm for [IGL.g@-ext] * STAR-Fusion complete. See output: /tmp/nxf.PqgL0O5dH7/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)