[2026-06-03T20:01:43] Launching Arriba 2.4.0
[2026-06-03T20:01:43] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:02:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:02:07] Reading chimeric alignments from 'aih-tih-sc-13d441-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=8826267)
[2026-06-03T20:11:04] Marking multi-mapping alignments (marked=5692296)
[2026-06-03T20:11:08] Detecting strandedness (reverse)
[2026-06-03T20:11:08] Assigning strands to alignments 
[2026-06-03T20:11:10] Annotating alignments 
[2026-06-03T20:11:41] Filtering duplicates (remaining=5832060)
[2026-06-03T20:11:47] 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=5498904)
[2026-06-03T20:11:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5498904)
[2026-06-03T20:11:51] Filtering viral contigs with expression lower than the top 5 (remaining=5498904)
[2026-06-03T20:11:55] Filtering viral contigs with less than 5% coverage (remaining=5498904)
[2026-06-03T20:11:57] Estimating fragment length (mate gap mean=-85.2714, mate gap stddev=28.8927, read length mean=127.387)
[2026-06-03T20:11:57] Filtering read-through fragments with a distance <=10000bp (remaining=5120598)
[2026-06-03T20:11:59] Filtering inconsistently clipped mates (remaining=5014207)
[2026-06-03T20:12:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4866491)
[2026-06-03T20:12:05] Filtering fragments with small insert size (remaining=4865606)
[2026-06-03T20:12:06] Filtering alignments with long gaps (remaining=4865606)
[2026-06-03T20:12:08] Filtering fragments with both mates in the same gene (remaining=4864496)
[2026-06-03T20:12:10] Filtering fusions arising from hairpin structures (remaining=4540281)
[2026-06-03T20:12:12] Filtering reads with a mismatch p-value <=0.01 (remaining=1979551)
[2026-06-03T20:12:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=1010806)
[2026-06-03T20:12:34] Finding fusions and counting supporting reads (total=756681)
[2026-06-03T20:12:49] Merging adjacent fusion breakpoints (remaining=747561)
[2026-06-03T20:12:51] Filtering multi-mapping fusions by alignment score and read support (remaining=457807)
[2026-06-03T20:13:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:13:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=455736)
[2026-06-03T20:13:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=266188)
[2026-06-03T20:13:28] Filtering fusions with <2 supporting reads (remaining=34279)
[2026-06-03T20:13:29] Filtering fusions with an e-value >=0.3 (remaining=8748)
[2026-06-03T20:13:29] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8808)
[2026-06-03T20:13:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8701)
[2026-06-03T20:13:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8701)
[2026-06-03T20:13:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7999)
[2026-06-03T20:13:39] Searching for fusions with spliced split reads (remaining=8126)
[2026-06-03T20:13:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=5119)
[2026-06-03T20:13:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5066)
[2026-06-03T20:13:45] Searching for fusions with >=4 spliced events (remaining=5927)
[2026-06-03T20:13:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2019)
[2026-06-03T20:14:06] Filtering fusions with anchors <=23nt (remaining=1658)
[2026-06-03T20:14:06] Filtering end-to-end fusions with low support (remaining=1611)
[2026-06-03T20:14:07] Filtering fusions with no coverage around the breakpoints (remaining=1580)
[2026-06-03T20:14:07] Indexing gene sequences 
[2026-06-03T20:14:14] Filtering genes with >=30% identity (remaining=447)
[2026-06-03T20:14:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=179)
[2026-06-03T20:14:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-03T20:14:24] Searching for additional isoforms (remaining=214)
[2026-06-03T20:14:25] Assigning confidence scores to events 
[2026-06-03T20:14:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:14:29] Writing fusions to file 'aih-tih-sc-13d441-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:14:31] Writing discarded fusions to file 'aih-tih-sc-13d441-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:15:05] Freeing resources
[2026-06-03T20:15:22] Done (elapsed time=00:13:39, CPU time=00:13:37, peak memory=13.6gb)