Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/dc2313720a9b5b0da8d060f9674d24/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_annot.gtf Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3 Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/dc2313720a9b5b0da8d060f9674d24/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/4c6b847f10b449472a8dc629e88231/659_dKM-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam ==> STAGING COMPLETE (8 inputs) [2026-06-04T21:09:46] Launching Arriba 2.4.0 [2026-06-04T21:09:46] Loading assembly from 'ref_genome.fa' [2026-06-04T21:09:54] Loading annotation from 'ref_annot.gtf' [2026-06-04T21:09:58] Reading chimeric alignments from '659_dKM-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' WARNING: 70558 SAM records were malformed and ignored (total=10782533) [2026-06-04T21:16:40] Marking multi-mapping alignments (marked=6699122) [2026-06-04T21:16:45] Detecting strandedness (reverse) [2026-06-04T21:16:45] Assigning strands to alignments [2026-06-04T21:16:47] Annotating alignments [2026-06-04T21:17:22] Filtering duplicates (remaining=6965957) [2026-06-04T21:17:29] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=6609727) [2026-06-04T21:17:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6609727) [2026-06-04T21:17:34] Filtering viral contigs with expression lower than the top 5 (remaining=6609727) [2026-06-04T21:17:39] Filtering viral contigs with less than 5% coverage (remaining=6609727) [2026-06-04T21:17:41] Estimating fragment length (mate gap mean=-87.476, mate gap stddev=27.6882, read length mean=129.575) [2026-06-04T21:17:42] Filtering read-through fragments with a distance <=10000bp (remaining=6128461) [2026-06-04T21:17:44] Filtering inconsistently clipped mates (remaining=6042698) [2026-06-04T21:17:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5809242) [2026-06-04T21:17:51] Filtering fragments with small insert size (remaining=5808199) [2026-06-04T21:17:53] Filtering alignments with long gaps (remaining=5808199) [2026-06-04T21:17:56] Filtering fragments with both mates in the same gene (remaining=5807291) [2026-06-04T21:17:58] Filtering fusions arising from hairpin structures (remaining=5533169) [2026-06-04T21:18:01] Filtering reads with a mismatch p-value <=0.01 (remaining=2860200) [2026-06-04T21:18:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=1433460) [2026-06-04T21:18:27] Finding fusions and counting supporting reads (total=WARNING: some fusions were subsampled, because they have more than 300 supporting reads 1022024) [2026-06-04T21:18:44] Merging adjacent fusion breakpoints (remaining=1010061) [2026-06-04T21:18:46] Filtering multi-mapping fusions by alignment score and read support (remaining=619633) [2026-06-04T21:19:19] Estimating expected number of fusions by random chance (e-value) [2026-06-04T21:19:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=618097) [2026-06-04T21:19:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=349052) [2026-06-04T21:19:29] Filtering fusions with <2 supporting reads (remaining=48901) [2026-06-04T21:19:30] Filtering fusions with an e-value >=0.3 (remaining=10600) [2026-06-04T21:19:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10638) [2026-06-04T21:19:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10522) [2026-06-04T21:19:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10522) [2026-06-04T21:19:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9728) [2026-06-04T21:19:42] Searching for fusions with spliced split reads (remaining=9851) [2026-06-04T21:19:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=5814) [2026-06-04T21:19:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5765) [2026-06-04T21:19:50] Searching for fusions with >=4 spliced events (remaining=7420) [2026-06-04T21:19:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3032) [2026-06-04T21:20:06] Filtering fusions with anchors <=23nt (remaining=2538) [2026-06-04T21:20:07] Filtering end-to-end fusions with low support (remaining=2487) [2026-06-04T21:20:07] Filtering fusions with no coverage around the breakpoints (remaining=2413) [2026-06-04T21:20:08] Indexing gene sequences [2026-06-04T21:20:15] Filtering genes with >=30% identity (remaining=757) [2026-06-04T21:20:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=370) [2026-06-04T21:20:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=273) [2026-06-04T21:20:25] Searching for additional isoforms (remaining=397) [2026-06-04T21:20:26] Assigning confidence scores to events [2026-06-04T21:20:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3' WARNING: unknown gene: CENPS-CORT ENSG00000251503 WARNING: unknown gene: P3R3URF-PIK3R3 ENSG00000278139 WARNING: unknown gene: FPGT-TNNI3K ENSG00000259030 WARNING: unknown gene: ENSG00000267561 WARNING: unknown gene: TLCD4-RWDD3 ENSG00000271092 WARNING: unknown gene: ENSG00000283761 WARNING: unknown gene: ENSG00000286185 WARNING: unknown gene: ENSG00000251246 WARNING: unknown gene: PMF1-BGLAP ENSG00000260238 WARNING: unknown gene: ENSG00000284299 WARNING: unknown gene: ENSG00000255835 WARNING: unknown gene: ENSG00000287856 WARNING: unknown gene: ENSG00000239395 WARNING: unknown gene: NT5C1B-RDH14 ENSG00000250741 WARNING: unknown gene: ENSG00000258881 WARNING: unknown gene: RNF103-CHMP3 ENSG00000249884 WARNING: unknown gene: ENSG00000273155 WARNING: unknown gene: LY75-CD302 ENSG00000248672 WARNING: unknown gene: ENSG00000251569 WARNING: unknown gene: HSPE1-MOB4 ENSG00000270757 WARNING: unknown gene: ARPC4-TTLL3 ENSG00000250151 WARNING: unknown gene: ENSG00000206549 WARNING: unknown gene: ENSG00000283189 WARNING: unknown gene: ABHD14A-ACY1 ENSG00000114786 WARNING: unknown gene: STIMATE-MUSTN1 ENSG00000248592 WARNING: unknown gene: ENSG00000285708 WARNING: unknown gene: ENSG00000285585 WARNING: unknown gene: ISY1-RAB43 ENSG00000261796 WARNING: unknown gene: ENSG00000285218 WARNING: unknown gene: ENSG00000275163 WARNING: unknown gene: ENSG00000283765 WARNING: unknown gene: EEF1AKMT4-ECE2 ENSG00000284917 WARNING: unknown gene: ENSG00000282278 WARNING: unknown gene: FAM47E-STBD1 ENSG00000272414 WARNING: unknown gene: ENSG00000285458 WARNING: unknown gene: ENSG00000287542 WARNING: unknown gene: ENSG00000285330 WARNING: unknown gene: ENSG00000284762 WARNING: unknown gene: TMED7-TICAM2 ENSG00000251201 WARNING: unknown gene: ENSG00000273217 WARNING: unknown gene: ENSG00000283782 WARNING: unknown gene: ANKHD1-EIF4EBP3 ENSG00000254996 WARNING: unknown gene: ENSG00000275740 WARNING: unknown gene: ENSG00000282988 WARNING: unknown gene: TRIM39-RPP21 ENSG00000248167 WARNING: unknown gene: ENSG00000263020 WARNING: unknown gene: LY6G6F-LY6G6D ENSG00000250641 WARNING: unknown gene: ENSG00000244255 WARNING: unknown gene: ENSG00000285446 WARNING: unknown gene: ENSG00000288520 WARNING: unknown gene: RBAK-RBAKDN ENSG00000272968 WARNING: unknown gene: ENSG00000283321 WARNING: unknown gene: ENSG00000257184 WARNING: unknown gene: ENSG00000281039 WARNING: unknown gene: ENSG00000256646 WARNING: unknown gene: ENSG00000249773 WARNING: unknown gene: ENSG00000284292 WARNING: unknown gene: ATP5MF-PTCD1 ENSG00000248919 WARNING: unknown gene: FMC1-LUC7L2 ENSG00000269955 WARNING: unknown gene: GIMAP1-GIMAP5 ENSG00000281887 WARNING: unknown gene: ABCF2-H2BE1 ENSG00000285292 WARNING: unknown gene: ENSG00000248235 WARNING: unknown gene: ENSG00000285880 WARNING: unknown gene: C8orf44-SGK3 ENSG00000288602 WARNING: unknown gene: ENSG00000285982 WARNING: unknown gene: ZHX1-C8orf76 ENSG00000259305 WARNING: unknown gene: ENSG00000258417 WARNING: unknown gene: LYNX1-SLURP2 ENSG00000284505 WARNING: unknown gene: ENSG00000264668 WARNING: unknown gene: ENSG00000288684 WARNING: unknown gene: MSANTD3-TMEFF1 ENSG00000251349 WARNING: unknown gene: DNAJC25-GNG10 ENSG00000244115 WARNING: unknown gene: ENSG00000286112 WARNING: unknown gene: ENSG00000235007 WARNING: unknown gene: PRRC2B ENSG00000288701 WARNING: unknown gene: ENSG00000285245 WARNING: unknown gene: COMMD3-BMI1 ENSG00000269897 WARNING: unknown gene: ENSG00000249967 WARNING: unknown gene: ENSG00000250644 WARNING: unknown gene: INS-IGF2 ENSG00000129965 WARNING: unknown gene: ENSG00000284931 WARNING: unknown gene: TRIM6-TRIM34 ENSG00000258588 WARNING: unknown gene: SAA2-SAA4 ENSG00000255071 WARNING: unknown gene: ENSG00000285283 WARNING: unknown gene: ENSG00000284732 WARNING: unknown gene: ENSG00000255432 WARNING: unknown gene: ENSG00000256349 WARNING: unknown gene: RBM14-RBM4 ENSG00000248643 WARNING: unknown gene: ENSG00000256514 WARNING: unknown gene: ENSG00000284922 WARNING: unknown gene: NDUFC2-KCTD14 ENSG00000259112 WARNING: unknown gene: ENSG00000284057 WARNING: unknown gene: ENSG00000258529 WARNING: unknown gene: FXYD6-FXYD2 ENSG00000255245 WARNING: unknown gene: ENSG00000285827 WARNING: unknown gene: ENSG00000255639 WARNING: unknown gene: ENSG00000255641 WARNING: unknown gene: SLCO1B3-SLCO1B7 ENSG00000257046 WARNING: unknown gene: ENSG00000272822 WARNING: unknown gene: ATF7-NPFF ENSG00000267281 WARNING: unknown gene: ENSG00000273049 WARNING: unknown gene: ENSG00000258311 WARNING: unknown gene: POC1B-GALNT4 ENSG00000259075 WARNING: unknown gene: ENSG00000256825 WARNING: unknown gene: CCDC169-SOHLH2 ENSG00000250709 WARNING: unknown gene: ENSG00000197991 WARNING: unknown gene: ENSG00000283208 WARNING: unknown gene: BIVM-ERCC5 ENSG00000270181 WARNING: unknown gene: ENSG00000254692 WARNING: unknown gene: CHURC1-FNTB ENSG00000125954 WARNING: unknown gene: SYNJ2BP-COX16 ENSG00000258644 WARNING: unknown gene: ENSG00000256500 WARNING: unknown gene: ENSG00000285472 WARNING: unknown gene: ENSG00000285920 WARNING: unknown gene: JMJD7-PLA2G4B ENSG00000168970 WARNING: unknown gene: ENSG00000285253 WARNING: unknown gene: ST20-MTHFS ENSG00000259332 WARNING: unknown gene: ENSG00000260836 WARNING: unknown gene: ENSG00000173867 WARNING: unknown gene: ARPIN-AP3S2 ENSG00000250021 WARNING: unknown gene: ENSG00000260272 WARNING: unknown gene: CORO7-PAM16 ENSG00000103426 WARNING: unknown gene: ENSG00000272617 WARNING: unknown gene: ENSG00000260537 WARNING: unknown gene: ENSG00000286221 WARNING: unknown gene: ENSG00000284512 WARNING: unknown gene: ENSG00000260643 WARNING: unknown gene: ENSG00000198211 WARNING: unknown gene: TNFSF12-TNFSF13 ENSG00000248871 WARNING: unknown gene: TVP23C-CDRT4 ENSG00000259024 WARNING: unknown gene: ENSG00000251537 WARNING: unknown gene: ENSG00000266202 WARNING: unknown gene: ENSG00000273171 WARNING: unknown gene: ENSG00000265118 WARNING: unknown gene: ENSG00000267618 WARNING: unknown gene: PTGES3L-AARSD1 ENSG00000108825 WARNING: unknown gene: LINC02210-CRHR1 ENSG00000263715 WARNING: unknown gene: NME1-NME2 ENSG00000011052 WARNING: unknown gene: ENSG00000265303 WARNING: unknown gene: ENSG00000267168 WARNING: unknown gene: ENSG00000262660 WARNING: unknown gene: RPL17-C18orf32 ENSG00000215472 WARNING: unknown gene: ZNF559-ZNF177 ENSG00000270011 WARNING: unknown gene: PPAN-P2RY11 ENSG00000243207 WARNING: unknown gene: ENSG00000267179 WARNING: unknown gene: ENSG00000286098 WARNING: unknown gene: ENSG00000196826 WARNING: unknown gene: ENSG00000285188 WARNING: unknown gene: BORCS8-MEF2B ENSG00000064489 WARNING: unknown gene: ENSG00000258674 WARNING: unknown gene: ENSG00000285526 WARNING: unknown gene: ENSG00000255730 WARNING: unknown gene: APOC4-APOC2 ENSG00000224916 WARNING: unknown gene: ZNF816-ZNF321P ENSG00000221874 WARNING: unknown gene: ENSG00000260861 WARNING: unknown gene: ENSG00000286022 WARNING: unknown gene: ENSG00000241690 WARNING: unknown gene: ENSG00000286235 WARNING: unknown gene: ENSG00000285382 WARNING: unknown gene: TGIF2-RAB5IF ENSG00000259399 WARNING: unknown gene: EPPIN-WFDC6 ENSG00000249139 WARNING: unknown gene: PEDS1-UBE2V1 ENSG00000124208 WARNING: unknown gene: CFAP298-TCP10L ENSG00000265590 WARNING: unknown gene: GET1-SH3BGR ENSG00000285815 WARNING: unknown gene: ENSG00000283809 WARNING: unknown gene: IGLL5 ENSG00000254709 WARNING: unknown gene: ENSG00000251357 WARNING: unknown gene: ENSG00000285762 WARNING: unknown gene: ENSG00000248751 WARNING: unknown gene: ENSG00000249590 WARNING: unknown gene: ENSG00000285404 WARNING: unknown gene: ENSG00000285304 WARNING: unknown gene: TPTEP2-CSNK1E ENSG00000283900 WARNING: unknown gene: ENSG00000284554 WARNING: unknown gene: PRR5-ARHGAP8 ENSG00000248405 WARNING: unknown gene: ENSG00000250349 WARNING: unknown gene: ENSG00000286268 WARNING: unknown gene: ENSG00000288053 WARNING: unknown gene: RPL36A-HNRNPH2 ENSG00000257529 WARNING: unknown gene: ENSG00000241489 [2026-06-04T21:20:30] Writing fusions to file '659_dKM-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' WARNING: encountered early stop codon in transcript ENST00000465370.1 at amino acid 41 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000465370.1 at amino acid 41 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000465370.1 at amino acid 41 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000573519.5 at amino acid 7 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000572824.1 at amino acid 58 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000581400.2 at amino acid 9 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000581400.2 at amino acid 9 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000581400.2 at amino acid 9 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000581400.2 at amino acid 9 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000581400.2 at amino acid 9 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000581400.2 at amino acid 9 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000581400.2 at amino acid 9 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000581400.2 at amino acid 9 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000639853.1 at amino acid 36 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000639853.1 at amino acid 36 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000639853.1 at amino acid 36 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000639853.1 at amino acid 36 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000639853.1 at amino acid 36 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000639853.1 at amino acid 36 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000639853.1 at amino acid 36 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000639853.1 at amino acid 36 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000639853.1 at amino acid 36 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000639853.1 at amino acid 36 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000473961.5 at amino acid 26 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000412061.3 at amino acid 17 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000473961.5 at amino acid 26 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000412061.3 at amino acid 17 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000473961.5 at amino acid 26 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000412061.3 at amino acid 17 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000473961.5 at amino acid 26 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000412061.3 at amino acid 17 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000448034.5 at amino acid 21 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000448034.5 at amino acid 21 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000448034.5 at amino acid 21 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000448034.5 at amino acid 21 (error in GTF file?) => predicted peptide sequence may be wrong WARNING: encountered early stop codon in transcript ENST00000448034.5 at amino acid 21 (error in GTF file?) => predicted peptide sequence may be wrong [2026-06-04T21:20:33] Writing discarded fusions to file '659_dKM-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv' [2026-06-04T21:21:02] Freeing resources [2026-06-04T21:21:21] Done (elapsed time=00:11:35, CPU time=00:11:33, peak memory=15.6gb)