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/3a/05da3385264a29e4ac6dd578ad9318/.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/3a/05da3385264a29e4ac6dd578ad9318/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/444a4a563b71eaad4fb7edb5ef1214/tih_rna_sample_00088_23H5VFLT4_s02.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (8 inputs)

[2026-06-08T08:30:38] Launching Arriba 2.4.0
[2026-06-08T08:30:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:52] Reading chimeric alignments from 'tih_rna_sample_00088_23H5VFLT4_s02.Aligned.sortedByCoord.out.bam' (total=WARNING: 112807 SAM records were malformed and ignored
11377887)
[2026-06-08T08:39:06] Marking multi-mapping alignments (marked=7678632)
[2026-06-08T08:39:12] Detecting strandedness (no)
[2026-06-08T08:39:12] Annotating alignments 
[2026-06-08T08:40:11] Filtering duplicates (remaining=6558742)
[2026-06-08T08:40:21] 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=5935145)
[2026-06-08T08:40:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5935145)
[2026-06-08T08:40:27] Filtering viral contigs with expression lower than the top 5 (remaining=5935145)
[2026-06-08T08:40:34] Filtering viral contigs with less than 5% coverage (remaining=5935145)
[2026-06-08T08:40:37] Estimating fragment length (mate gap mean=-86.2046, mate gap stddev=30.177, read length mean=126.208)
[2026-06-08T08:40:37] Filtering read-through fragments with a distance <=10000bp (remaining=5604037)
[2026-06-08T08:40:40] Filtering inconsistently clipped mates (remaining=5460390)
[2026-06-08T08:40:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5064894)
[2026-06-08T08:40:50] Filtering fragments with small insert size (remaining=5062812)
[2026-06-08T08:40:52] Filtering alignments with long gaps (remaining=5062812)
[2026-06-08T08:40:56] Filtering fragments with both mates in the same gene (remaining=5061314)
[2026-06-08T08:40:59] Filtering fusions arising from hairpin structures (remaining=4530533)
[2026-06-08T08:41:03] Filtering reads with a mismatch p-value <=0.01 (remaining=1681917)
[2026-06-08T08:41:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=997927)
[2026-06-08T08:41:30] Finding fusions and counting supporting reads WARNING: some fusions were subsampled, because they have more than 300 supporting reads
(total=838881)
[2026-06-08T08:41:52] Merging adjacent fusion breakpoints (remaining=828671)
[2026-06-08T08:41:54] Filtering multi-mapping fusions by alignment score and read support (remaining=475152)
[2026-06-08T08:42:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=472417)
[2026-06-08T08:42:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=287786)
[2026-06-08T08:42:54] Filtering fusions with <2 supporting reads (remaining=23216)
[2026-06-08T08:42:55] Filtering fusions with an e-value >=0.3 (remaining=4661)
[2026-06-08T08:42:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4737)
[2026-06-08T08:43:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4573)
[2026-06-08T08:43:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4573)
[2026-06-08T08:43:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4367)
[2026-06-08T08:43:14] Searching for fusions with spliced split reads (remaining=4467)
[2026-06-08T08:43:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=2944)
[2026-06-08T08:43:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2910)
[2026-06-08T08:43:25] Searching for fusions with >=4 spliced events (remaining=3370)
[2026-06-08T08:43:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1338)
[2026-06-08T08:43:44] Filtering fusions with anchors <=23nt (remaining=1039)
[2026-06-08T08:43:45] Filtering end-to-end fusions with low support (remaining=1019)
[2026-06-08T08:43:46] Filtering fusions with no coverage around the breakpoints (remaining=1000)
[2026-06-08T08:43:47] Indexing gene sequences 
[2026-06-08T08:43:55] Filtering genes with >=30% identity (remaining=323)
[2026-06-08T08:43:59] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=160)
[2026-06-08T08:44:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=142)
[2026-06-08T08:44:05] Searching for additional isoforms (remaining=183)
[2026-06-08T08:44:07] Assigning confidence scores to events 
[2026-06-08T08:44:12] 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
[2026-06-08T08:44:12] Writing fusions to file 'tih_rna_sample_00088_23H5VFLT4_s02.arriba.fusions.tsv' 
WARNING: encountered early stop codon in transcript ENST00000561947.5 at amino acid 2 (error in GTF file?) => predicted peptide sequence may be wrong
[2026-06-08T08:44:14] Writing discarded fusions to file 'tih_rna_sample_00088_23H5VFLT4_s02.arriba.fusions.discarded.tsv'
[2026-06-08T08:45:02] Freeing resources
[2026-06-08T08:45:32] Done (elapsed time=00:14:54, CPU time=00:14:53, peak memory=16.6gb)