[2026-06-08T08:46:33] Launching Arriba 2.4.0
[2026-06-08T08:46:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:52] Reading chimeric alignments from 'tih_rna_sample_00145_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=11231746)
[2026-06-08T08:54:39] Marking multi-mapping alignments (marked=7178066)
[2026-06-08T08:54:44] Detecting strandedness (reverse)
[2026-06-08T08:54:44] Assigning strands to alignments 
[2026-06-08T08:54:46] Annotating alignments 
[2026-06-08T08:55:25] Filtering duplicates (remaining=4618402)
[2026-06-08T08:55:32] 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=4369723)
[2026-06-08T08:55:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4369723)
[2026-06-08T08:55:37] Filtering viral contigs with expression lower than the top 5 (remaining=4369723)
[2026-06-08T08:55:42] Filtering viral contigs with less than 5% coverage (remaining=4369723)
[2026-06-08T08:55:44] Estimating fragment length (mate gap mean=-85.7968, mate gap stddev=27.2932, read length mean=124.519)
[2026-06-08T08:55:44] Filtering read-through fragments with a distance <=10000bp (remaining=4012997)
[2026-06-08T08:55:47] Filtering inconsistently clipped mates (remaining=3937241)
[2026-06-08T08:55:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3824849)
[2026-06-08T08:55:53] Filtering fragments with small insert size (remaining=3823788)
[2026-06-08T08:55:56] Filtering alignments with long gaps (remaining=3823788)
[2026-06-08T08:55:59] Filtering fragments with both mates in the same gene (remaining=3823044)
[2026-06-08T08:56:01] Filtering fusions arising from hairpin structures (remaining=3628340)
[2026-06-08T08:56:04] Filtering reads with a mismatch p-value <=0.01 (remaining=1464680)
[2026-06-08T08:56:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=695959)
[2026-06-08T08:56:23] Finding fusions and counting supporting reads (total=600603)
[2026-06-08T08:56:41] Merging adjacent fusion breakpoints (remaining=592921)
[2026-06-08T08:56:42] Filtering multi-mapping fusions by alignment score and read support (remaining=353768)
[2026-06-08T08:57:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=352162)
[2026-06-08T08:57:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=183090)
[2026-06-08T08:57:28] Filtering fusions with <2 supporting reads (remaining=19519)
[2026-06-08T08:57:29] Filtering fusions with an e-value >=0.3 (remaining=4433)
[2026-06-08T08:57:29] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4480)
[2026-06-08T08:57:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4415)
[2026-06-08T08:57:34] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4415)
[2026-06-08T08:57:35] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4243)
[2026-06-08T08:57:40] Searching for fusions with spliced split reads (remaining=4291)
[2026-06-08T08:57:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=2960)
[2026-06-08T08:57:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2926)
[2026-06-08T08:57:47] Searching for fusions with >=4 spliced events (remaining=3380)
[2026-06-08T08:57:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1373)
[2026-06-08T08:58:02] Filtering fusions with anchors <=23nt (remaining=1138)
[2026-06-08T08:58:02] Filtering end-to-end fusions with low support (remaining=1114)
[2026-06-08T08:58:03] Filtering fusions with no coverage around the breakpoints (remaining=1085)
[2026-06-08T08:58:04] Indexing gene sequences 
[2026-06-08T08:58:08] Filtering genes with >=30% identity (remaining=338)
[2026-06-08T08:58:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=99)
[2026-06-08T08:58:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=99)
[2026-06-08T08:58:12] Searching for additional isoforms (remaining=118)
[2026-06-08T08:58:13] Assigning confidence scores to events 
[2026-06-08T08:58:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:16] Writing fusions to file 'tih_rna_sample_00145_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:58:17] Writing discarded fusions to file 'tih_rna_sample_00145_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:43] Freeing resources
[2026-06-08T08:59:01] Done (elapsed time=00:12:28, CPU time=00:12:26, peak memory=15.8gb)