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)