Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/7774b931aa4e760e2d3061827652ee/rna_s1221_S42_1.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/ce/868cbf881945487f1aac4aaa626fa4/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/4be880eb6bc2edc369423e8ed7f0cb/rna_s1221_S42.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/868cbf881945487f1aac4aaa626fa4/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/7774b931aa4e760e2d3061827652ee/rna_s1221_S42_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.aRBaN8bNVE/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.aRBaN8bNVE/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.aRBaN8bNVE/./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.aRBaN8bNVE/ctat_genome_lib_build_dir -J /tmp/nxf.aRBaN8bNVE/rna_s1221_S42.Chimeric.out.junction -O /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.aRBaN8bNVE/rna_s1221_S42.Chimeric.out.junction -building interval tree based on /tmp/nxf.aRBaN8bNVE/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.05 min). -mapping reads to genes [10000], rate=120000.00/min [20000], rate=200000.00/min [30000], rate=257142.86/min [40000], rate=300000.00/min [50000], rate=272727.27/min [60000], rate=200000.00/min [70000], rate=182608.70/min [80000], rate=165517.24/min [90000], rate=168750.00/min [100000], rate=181818.18/min [110000], rate=194117.65/min [120000], rate=205714.29/min [130000], rate=195000.00/min -building interval tree based on /tmp/nxf.aRBaN8bNVE/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=163636.36/min [40000], rate=133333.33/min [50000], rate=150000.00/min [60000], rate=150000.00/min [70000], rate=140000.00/min [80000], rate=154838.71/min [90000], rate=142105.26/min [100000], rate=139534.88/min [110000], rate=143478.26/min [120000], rate=118032.79/min [130000], rate=106849.32/min -building interval tree based on /tmp/nxf.aRBaN8bNVE/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=82758.62/min [90000], rate=81818.18/min [100000], rate=80000.00/min [110000], rate=80487.80/min [120000], rate=80000.00/min [130000], rate=81250.00/min -building interval tree based on /tmp/nxf.aRBaN8bNVE/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=70588.24/min [30000], rate=64285.71/min [40000], rate=68571.43/min [50000], rate=71428.57/min [60000], rate=72000.00/min [70000], rate=70000.00/min [80000], rate=70588.24/min [90000], rate=70129.87/min [100000], rate=70588.24/min [110000], rate=69473.68/min [120000], rate=67924.53/min [130000], rate=69642.86/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.aRBaN8bNVE/ctat_genome_lib_build_dir --filt_file /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.aRBaN8bNVE/./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... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.aRBaN8bNVE/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.aRBaN8bNVE/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.aRBaN8bNVE/./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.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.aRBaN8bNVE/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.aRBaN8bNVE/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.aRBaN8bNVE/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.aRBaN8bNVE/./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.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.aRBaN8bNVE/./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.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9928008 > /tmp/nxf.aRBaN8bNVE/./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.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.aRBaN8bNVE/ctat_genome_lib_build_dir > /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.aRBaN8bNVE/ctat_genome_lib_build_dir --annotate /tmp/nxf.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.aRBaN8bNVE/./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.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.aRBaN8bNVE/ctat_genome_lib_build_dir -done, see /tmp/nxf.aRBaN8bNVE/./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.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.aRBaN8bNVE/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.aRBaN8bNVE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.aRBaN8bNVE/./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.aRBaN8bNVE/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] WARNING, no entry stored in dbm for [ENSG00000257612.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000219665.8] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000226419.8] WARNING, no entry stored in dbm for [ENSG00000249726.1] WARNING, no entry stored in dbm for [ENSG00000250501.3] WARNING, no entry stored in dbm for [ENSG00000272625.1] WARNING, no entry stored in dbm for [ENSG00000241316.8] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000260676.5] WARNING, no entry stored in dbm for [ENSG00000286720.1] WARNING, no entry stored in dbm for [ENSG00000238061.2] WARNING, no entry stored in dbm for [ENSG00000259479.6] WARNING, no entry stored in dbm for [ENSG00000259479.6] WARNING, no entry stored in dbm for [ENSG00000285898.1] WARNING, no entry stored in dbm for [ENSG00000263934.5] WARNING, no entry stored in dbm for [ENSG00000269893.8] WARNING, no entry stored in dbm for [ENSG00000250988.7] WARNING, no entry stored in dbm for [ENSG00000260727.2] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000287411.1] WARNING, no entry stored in dbm for [ENSG00000223508.5] WARNING, no entry stored in dbm for [ENSG00000274210.1] WARNING, no entry stored in dbm for [ENSG00000287011.1] WARNING, no entry stored in dbm for [ENSG00000228940.1] WARNING, no entry stored in dbm for [ENSG00000238098.9] WARNING, no entry stored in dbm for [ENSG00000201793.1] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000200783.1] WARNING, no entry stored in dbm for [ENSG00000199691.1] WARNING, no entry stored in dbm for [ENSG00000201715.1] WARNING, no entry stored in dbm for [ENSG00000271394.1] WARNING, no entry stored in dbm for [ENSG00000245532.9] WARNING, no entry stored in dbm for [ENSG00000275374.1] WARNING, no entry stored in dbm for [ENSG00000236051.7] WARNING, no entry stored in dbm for [ENSG00000223612.3] WARNING, no entry stored in dbm for [ENSG00000269473.1] WARNING, no entry stored in dbm for [ENSG00000204352.4] WARNING, no entry stored in dbm for [ENSG00000235366.2] WARNING, no entry stored in dbm for [ENSG00000235314.1] WARNING, no entry stored in dbm for [ENSG00000237181.1] WARNING, no entry stored in dbm for [ENSG00000227882.1] 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 [ENSG00000248527.1] 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 [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 [ENSG00000225851.1] WARNING, no entry stored in dbm for [ENSG00000235527.7] WARNING, no entry stored in dbm for [ENSG00000225978.3] WARNING, no entry stored in dbm for [ENSG00000198555.7] WARNING, no entry stored in dbm for [ENSG00000250959.2] WARNING, no entry stored in dbm for [ENSG00000196295.12] WARNING, no entry stored in dbm for [ENSG00000272888.7] WARNING, no entry stored in dbm for [ENSG00000226688.7] WARNING, no entry stored in dbm for [ENSG00000170919.16] WARNING, no entry stored in dbm for [ENSG00000259002.2] WARNING, no entry stored in dbm for [ENSG00000278903.3] WARNING, no entry stored in dbm for [ENSG00000254231.3] WARNING, no entry stored in dbm for [ENSG00000270714.1] WARNING, no entry stored in dbm for [ENSG00000285417.1] WARNING, no entry stored in dbm for [ENSG00000229956.11] WARNING, no entry stored in dbm for [ENSG00000257252.6] WARNING, no entry stored in dbm for [ENSG00000243069.8] WARNING, no entry stored in dbm for [ENSG00000258096.1] WARNING, no entry stored in dbm for [ENSG00000256196.2] WARNING, no entry stored in dbm for [ENSG00000263884.1] WARNING, no entry stored in dbm for [ENSG00000228436.3] WARNING, no entry stored in dbm for [ENSG00000273162.1] WARNING, no entry stored in dbm for [ENSG00000253785.1] WARNING, no entry stored in dbm for [ENSG00000286912.1] WARNING, no entry stored in dbm for [ENSG00000283453.2] WARNING, no entry stored in dbm for [ENSG00000223991.1] WARNING, no entry stored in dbm for [ENSG00000239969.5] WARNING, no entry stored in dbm for [ENSG00000225205.5] WARNING, no entry stored in dbm for [ENSG00000257337.7] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000286011.1] WARNING, no entry stored in dbm for [ENSG00000216895.9] 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 [ENSG00000272369.1] WARNING, no entry stored in dbm for [ENSG00000269968.1] * STAR-Fusion complete. See output: /tmp/nxf.aRBaN8bNVE/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)