Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/15963dba4d935ffd3d52b93bfc4e41/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/ac109c0031aa049abdc246b4535984/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1_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/ae/53b45c8371fa6a43fcad7c6ab2352b/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/53b45c8371fa6a43fcad7c6ab2352b/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/ac109c0031aa049abdc246b4535984/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.0jMiK3qXRn/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary -sample contains 9824221 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir -J /tmp/nxf.0jMiK3qXRn/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction -O /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.0jMiK3qXRn/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=37500.00/min [20000], rate=40000.00/min [30000], rate=36734.69/min [40000], rate=38709.68/min [50000], rate=41666.67/min [60000], rate=43902.44/min [70000], rate=46153.85/min [80000], rate=51063.83/min [90000], rate=54000.00/min [100000], rate=58823.53/min [110000], rate=62857.14/min [120000], rate=63716.81/min [130000], rate=67826.09/min [140000], rate=69421.49/min [150000], rate=71428.57/min [160000], rate=72180.45/min [170000], rate=75000.00/min [180000], rate=78832.12/min [190000], rate=77551.02/min -building interval tree based on /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=40000.00/min [20000], rate=37500.00/min [30000], rate=39130.43/min [40000], rate=42105.26/min [50000], rate=42253.52/min [60000], rate=44444.44/min [70000], rate=44680.85/min [80000], rate=46153.85/min [90000], rate=46153.85/min [100000], rate=46153.85/min [110000], rate=46808.51/min [120000], rate=48000.00/min [130000], rate=48447.20/min [140000], rate=49122.81/min [150000], rate=48648.65/min [160000], rate=49484.54/min [170000], rate=51000.00/min [180000], rate=51428.57/min [190000], rate=53023.26/min -building interval tree based on /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=85714.29/min [30000], rate=94736.84/min [40000], rate=92307.69/min [50000], rate=107142.86/min [60000], rate=102857.14/min [70000], rate=102439.02/min [80000], rate=100000.00/min [90000], rate=100000.00/min [100000], rate=85714.29/min [110000], rate=70967.74/min [120000], rate=63716.81/min [130000], rate=60937.50/min [140000], rate=60869.57/min [150000], rate=60000.00/min [160000], rate=57831.33/min [170000], rate=54838.71/min [180000], rate=52682.93/min [190000], rate=52293.58/min -building interval tree based on /tmp/nxf.0jMiK3qXRn/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=38709.68/min [30000], rate=43902.44/min [40000], rate=45283.02/min [50000], rate=47619.05/min [60000], rate=47368.42/min [70000], rate=47191.01/min [80000], rate=46601.94/min [90000], rate=45762.71/min [100000], rate=45112.78/min [110000], rate=46478.87/min [120000], rate=45859.87/min [130000], rate=45348.84/min [140000], rate=44444.44/min [150000], rate=44117.65/min [160000], rate=45070.42/min [170000], rate=46363.64/min [180000], rate=45378.15/min [190000], rate=44881.89/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir --filt_file /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3428571.43 reads per min processed... 3333333.33 reads per min processed... 3600000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.0jMiK3qXRn/1173_QEV_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.0jMiK3qXRn/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -11852.442008 EM: Round [1] log likelihood: -11823.350898 EM: Round [2] log likelihood: -11810.332441 EM: Round [3] log likelihood: -11803.439017 EM: Round [4] log likelihood: -11799.644918 EM: Round [5] log likelihood: -11797.524680 EM: Round [6] log likelihood: -11796.312173 EM: Round [7] log likelihood: -11795.595375 EM: Round [8] log likelihood: -11795.155118 EM: Round [9] log likelihood: -11794.874127 EM: Round [10] log likelihood: -11794.688266 EM: Round [11] log likelihood: -11794.561345 EM: Round [12] log likelihood: -11794.472216 EM: Round [13] log likelihood: -11794.408079 EM: Round [14] log likelihood: -11794.360924 EM: Round [15] log likelihood: -11794.325586 EM: Round [16] log likelihood: -11794.298640 EM: Round [17] log likelihood: -11794.277761 EM: Round [18] log likelihood: -11794.261337 EM: Round [19] log likelihood: -11794.248233 EM: Round [20] log likelihood: -11794.237632 EM: Round [21] log likelihood: -11794.228941 EM: Round [22] log likelihood: -11794.221726 EM: Round [23] log likelihood: -11794.215661 EM: Round [24] log likelihood: -11794.210502 EM: Round [25] log likelihood: -11794.206064 EM: Round [26] log likelihood: -11794.202205 EM: Round [27] log likelihood: -11794.198817 EM: Round [28] log likelihood: -11794.195814 EM: Round [29] log likelihood: -11794.193130 EM: Round [30] log likelihood: -11794.190712 EM: Round [31] log likelihood: -11794.188519 EM: Round [32] log likelihood: -11794.186517 EM: Round [33] log likelihood: -11794.184680 EM: Round [34] log likelihood: -11794.182986 EM: Round [35] log likelihood: -11794.181418 EM: Round [36] log likelihood: -11794.179959 EM: Round [37] log likelihood: -11794.178599 EM: Round [38] log likelihood: -11794.177328 EM: Round [39] log likelihood: -11794.176136 EM: Round [40] log likelihood: -11794.175017 EM: Round [41] log likelihood: -11794.173963 EM: Round [42] log likelihood: -11794.172971 EM: Round [43] log likelihood: -11794.172035 EM: Round [44] log likelihood: -11794.171151 EM: Round [45] log likelihood: -11794.170316 EM: Round [46] log likelihood: -11794.169526 EM: Round [47] log likelihood: -11794.168778 EM: Round [48] log likelihood: -11794.168070 EM: Round [49] log likelihood: -11794.167399 EM: Round [50] log likelihood: -11794.166763 EM: Round [51] log likelihood: -11794.166161 EM: Round [52] log likelihood: -11794.165589 EM: Round [53] log likelihood: -11794.165047 EM: Round [54] log likelihood: -11794.164532 EM: Round [55] log likelihood: -11794.164044 EM: Round [56] log likelihood: -11794.163581 EM: Round [57] log likelihood: -11794.163142 EM: Round [58] log likelihood: -11794.162725 EM: Round [59] log likelihood: -11794.162329 EM: Round [60] log likelihood: -11794.161953 EM: Round [61] log likelihood: -11794.161596 EM: Round [62] log likelihood: -11794.161257 EM: Round [63] log likelihood: -11794.160935 EM: Round [64] log likelihood: -11794.160629 EM: Round [65] log likelihood: -11794.160339 EM: Round [66] log likelihood: -11794.160063 EM: Round [67] log likelihood: -11794.159801 EM: Round [68] log likelihood: -11794.159552 EM: Round [69] log likelihood: -11794.159316 EM: Round [70] log likelihood: -11794.159091 EM: Round [71] log likelihood: -11794.158878 EM: Round [72] log likelihood: -11794.158675 EM: Round [73] log likelihood: -11794.158483 EM: Round [74] log likelihood: -11794.158300 EM: Round [75] log likelihood: -11794.158126 EM: Round [76] log likelihood: -11794.157960 EM: Round [77] log likelihood: -11794.157803 EM: Round [78] log likelihood: -11794.157654 EM: Round [79] log likelihood: -11794.157511 EM: Round [80] log likelihood: -11794.157376 EM: Round [81] log likelihood: -11794.157248 EM: Round [82] log likelihood: -11794.157125 EM: Round [83] log likelihood: -11794.157009 EM: Round [84] log likelihood: -11794.156898 EM: Round [85] log likelihood: -11794.156793 EM: Round [86] log likelihood: -11794.156693 EM: Round [87] log likelihood: -11794.156598 EM: Stopping iterations at round 87 due to insufficient improvement in likelihood. EM: Starting log likelihood: -11847.597142 EM: Round [1] log likelihood: -11819.634612 EM: Round [2] log likelihood: -11807.834418 EM: Round [3] log likelihood: -11801.909458 EM: Round [4] log likelihood: -11798.728317 EM: Round [5] log likelihood: -11796.960972 EM: Round [6] log likelihood: -11795.947512 EM: Round [7] log likelihood: -11795.345047 EM: Round [8] log likelihood: -11794.972983 EM: Round [9] log likelihood: -11794.734585 EM: Round [10] log likelihood: -11794.576637 EM: Round [11] log likelihood: -11794.468869 EM: Round [12] log likelihood: -11794.393443 EM: Round [13] log likelihood: -11794.339476 EM: Round [14] log likelihood: -11794.300113 EM: Round [15] log likelihood: -11794.270911 EM: Round [16] log likelihood: -11794.248914 EM: Round [17] log likelihood: -11794.232111 EM: Round [18] log likelihood: -11794.219110 EM: Round [19] log likelihood: -11794.208928 EM: Round [20] log likelihood: -11794.200861 EM: Round [21] log likelihood: -11794.194399 EM: Round [22] log likelihood: -11794.189168 EM: Round [23] log likelihood: -11794.184890 EM: Round [24] log likelihood: -11794.181356 EM: Round [25] log likelihood: -11794.178409 EM: Round [26] log likelihood: -11794.175929 EM: Round [27] log likelihood: -11794.173823 EM: Round [28] log likelihood: -11794.172020 EM: Round [29] log likelihood: -11794.170463 EM: Round [30] log likelihood: -11794.169108 EM: Round [31] log likelihood: -11794.167921 EM: Round [32] log likelihood: -11794.166873 EM: Round [33] log likelihood: -11794.165943 EM: Round [34] log likelihood: -11794.165113 EM: Round [35] log likelihood: -11794.164367 EM: Round [36] log likelihood: -11794.163694 EM: Round [37] log likelihood: -11794.163084 EM: Round [38] log likelihood: -11794.162529 EM: Round [39] log likelihood: -11794.162022 EM: Round [40] log likelihood: -11794.161557 EM: Round [41] log likelihood: -11794.161130 EM: Round [42] log likelihood: -11794.160736 EM: Round [43] log likelihood: -11794.160372 EM: Round [44] log likelihood: -11794.160036 EM: Round [45] log likelihood: -11794.159723 EM: Round [46] log likelihood: -11794.159433 EM: Round [47] log likelihood: -11794.159163 EM: Round [48] log likelihood: -11794.158911 EM: Round [49] log likelihood: -11794.158676 EM: Round [50] log likelihood: -11794.158456 EM: Round [51] log likelihood: -11794.158251 EM: Round [52] log likelihood: -11794.158059 EM: Round [53] log likelihood: -11794.157879 EM: Round [54] log likelihood: -11794.157710 EM: Round [55] log likelihood: -11794.157552 EM: Round [56] log likelihood: -11794.157403 EM: Round [57] log likelihood: -11794.157263 EM: Round [58] log likelihood: -11794.157132 EM: Round [59] log likelihood: -11794.157008 EM: Round [60] log likelihood: -11794.156892 EM: Round [61] log likelihood: -11794.156782 EM: Round [62] log likelihood: -11794.156679 EM: Round [63] log likelihood: -11794.156582 EM: Stopping iterations at round 63 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9824221 > /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir > /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir --annotate /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir -done, see /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.0jMiK3qXRn/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 104, filtered: 1132) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.0jMiK3qXRn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.0jMiK3qXRn/./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.0jMiK3qXRn/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000234996.4] WARNING, no entry stored in dbm for [ENSG00000274712.2] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000280304.1] WARNING, no entry stored in dbm for [ENSG00000230559.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000254743.1] WARNING, no entry stored in dbm for [ENSG00000236596.1] WARNING, no entry stored in dbm for [ENSG00000224699.9] WARNING, no entry stored in dbm for [ENSG00000254034.2] 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 [ENSG00000273419.1] WARNING, no entry stored in dbm for [ENSG00000225851.1] WARNING, no entry stored in dbm for [ENSG00000250903.9] WARNING, no entry stored in dbm for [ENSG00000213409.4] WARNING, no entry stored in dbm for [ENSG00000158482.10] WARNING, no entry stored in dbm for [ENSG00000283849.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000254473.1] WARNING, no entry stored in dbm for [ENSG00000283480.1] WARNING, no entry stored in dbm for [ENSG00000261292.2] WARNING, no entry stored in dbm for [ENSG00000280828.1] WARNING, no entry stored in dbm for [ENSG00000286629.1] * STAR-Fusion complete. See output: /tmp/nxf.0jMiK3qXRn/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)