[2026-06-08T07:58:42] Launching Arriba 2.4.0
[2026-06-08T07:58:42] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:59:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:59:08] Reading chimeric alignments from 'aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=6003184)
[2026-06-08T08:03:40] Marking multi-mapping alignments (marked=4088441)
[2026-06-08T08:03:43] Detecting strandedness (reverse)
[2026-06-08T08:03:43] Assigning strands to alignments 
[2026-06-08T08:03:44] Annotating alignments 
[2026-06-08T08:04:08] Filtering duplicates (remaining=3235320)
[2026-06-08T08:04:16] 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=3078647)
[2026-06-08T08:04:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3078647)
[2026-06-08T08:04:19] Filtering viral contigs with expression lower than the top 5 (remaining=3078647)
[2026-06-08T08:04:22] Filtering viral contigs with less than 5% coverage (remaining=3078647)
[2026-06-08T08:04:23] Estimating fragment length (mate gap mean=-83.2657, mate gap stddev=27.0997, read length mean=122.235)
[2026-06-08T08:04:24] Filtering read-through fragments with a distance <=10000bp (remaining=2941095)
[2026-06-08T08:04:25] Filtering inconsistently clipped mates (remaining=2879984)
[2026-06-08T08:04:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2769021)
[2026-06-08T08:04:29] Filtering fragments with small insert size (remaining=2768449)
[2026-06-08T08:04:31] Filtering alignments with long gaps (remaining=2768449)
[2026-06-08T08:04:32] Filtering fragments with both mates in the same gene (remaining=2767738)
[2026-06-08T08:04:34] Filtering fusions arising from hairpin structures (remaining=2620628)
[2026-06-08T08:04:36] Filtering reads with a mismatch p-value <=0.01 (remaining=1169779)
[2026-06-08T08:04:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=387768)
[2026-06-08T08:04:51] Finding fusions and counting supporting reads (total=325120)
[2026-06-08T08:05:04] Merging adjacent fusion breakpoints (remaining=322675)
[2026-06-08T08:05:05] Filtering multi-mapping fusions by alignment score and read support (remaining=178438)
[2026-06-08T08:05:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:05:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=177689)
[2026-06-08T08:05:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=117894)
[2026-06-08T08:05:33] Filtering fusions with <2 supporting reads (remaining=10826)
[2026-06-08T08:05:34] Filtering fusions with an e-value >=0.3 (remaining=2603)
[2026-06-08T08:05:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2653)
[2026-06-08T08:05:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2601)
[2026-06-08T08:05:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2601)
[2026-06-08T08:05:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2577)
[2026-06-08T08:05:41] Searching for fusions with spliced split reads (remaining=2633)
[2026-06-08T08:05:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=1878)
[2026-06-08T08:05:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1856)
[2026-06-08T08:05:47] Searching for fusions with >=4 spliced events (remaining=2121)
[2026-06-08T08:05:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=795)
[2026-06-08T08:06:10] Filtering fusions with anchors <=23nt (remaining=681)
[2026-06-08T08:06:11] Filtering end-to-end fusions with low support (remaining=668)
[2026-06-08T08:06:11] Filtering fusions with no coverage around the breakpoints (remaining=653)
[2026-06-08T08:06:12] Indexing gene sequences 
[2026-06-08T08:06:16] Filtering genes with >=30% identity (remaining=196)
[2026-06-08T08:06:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=112)
[2026-06-08T08:06:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=106)
[2026-06-08T08:06:20] Searching for additional isoforms (remaining=128)
[2026-06-08T08:06:20] Assigning confidence scores to events 
[2026-06-08T08:06:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:06:23] Writing fusions to file 'aih-tih-sc-505123-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:06:24] Writing discarded fusions to file 'aih-tih-sc-505123-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:06:46] Freeing resources
[2026-06-08T08:07:01] Done (elapsed time=00:08:19, CPU time=00:08:17, peak memory=10.3gb)