[2026-06-03T20:35:47] Launching Arriba 2.4.0
[2026-06-03T20:35:47] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:35:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:35:58] Reading chimeric alignments from 'aih-tih-sc-b6fd19-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10904926)
[2026-06-03T20:42:50] Marking multi-mapping alignments (marked=7046722)
[2026-06-03T20:42:55] Detecting strandedness (reverse)
[2026-06-03T20:42:55] Assigning strands to alignments 
[2026-06-03T20:42:57] Annotating alignments 
[2026-06-03T20:43:32] Filtering duplicates (remaining=7118910)
[2026-06-03T20:43:39] 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=6597168)
[2026-06-03T20:43:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6597168)
[2026-06-03T20:43:44] Filtering viral contigs with expression lower than the top 5 (remaining=6597168)
[2026-06-03T20:43:49] Filtering viral contigs with less than 5% coverage (remaining=6597168)
[2026-06-03T20:43:52] Estimating fragment length (mate gap mean=-83.0544, mate gap stddev=31.1327, read length mean=131.701)
[2026-06-03T20:43:52] Filtering read-through fragments with a distance <=10000bp (remaining=6219385)
[2026-06-03T20:43:55] Filtering inconsistently clipped mates (remaining=6105350)
[2026-06-03T20:43:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5933128)
[2026-06-03T20:44:02] Filtering fragments with small insert size (remaining=5932173)
[2026-06-03T20:44:04] Filtering alignments with long gaps (remaining=5932173)
[2026-06-03T20:44:06] Filtering fragments with both mates in the same gene (remaining=5930613)
[2026-06-03T20:44:09] Filtering fusions arising from hairpin structures (remaining=5534046)
[2026-06-03T20:44:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2573373)
[2026-06-03T20:44:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=1268248)
[2026-06-03T20:44:38] Finding fusions and counting supporting reads (total=872240)
[2026-06-03T20:44:55] Merging adjacent fusion breakpoints (remaining=865032)
[2026-06-03T20:44:57] Filtering multi-mapping fusions by alignment score and read support (remaining=561016)
[2026-06-03T20:45:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:45:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=557933)
[2026-06-03T20:45:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=325840)
[2026-06-03T20:45:38] Filtering fusions with <2 supporting reads (remaining=52260)
[2026-06-03T20:45:39] Filtering fusions with an e-value >=0.3 (remaining=18244)
[2026-06-03T20:45:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=18291)
[2026-06-03T20:45:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=18200)
[2026-06-03T20:45:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=18200)
[2026-06-03T20:45:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=11138)
[2026-06-03T20:45:52] Searching for fusions with spliced split reads (remaining=11193)
[2026-06-03T20:45:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=5827)
[2026-06-03T20:45:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5760)
[2026-06-03T20:45:59] Searching for fusions with >=4 spliced events (remaining=7079)
[2026-06-03T20:46:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2758)
[2026-06-03T20:46:17] Filtering fusions with anchors <=23nt (remaining=2228)
[2026-06-03T20:46:18] Filtering end-to-end fusions with low support (remaining=2154)
[2026-06-03T20:46:18] Filtering fusions with no coverage around the breakpoints (remaining=2106)
[2026-06-03T20:46:19] Indexing gene sequences 
[2026-06-03T20:46:29] Filtering genes with >=30% identity (remaining=989)
[2026-06-03T20:46:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=671)
[2026-06-03T20:46:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=459)
[2026-06-03T20:46:48] Searching for additional isoforms (remaining=667)
[2026-06-03T20:46:49] Assigning confidence scores to events 
[2026-06-03T20:46:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:46:53] Writing fusions to file 'aih-tih-sc-b6fd19-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:46:58] Writing discarded fusions to file 'aih-tih-sc-b6fd19-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:47:27] Freeing resources
[2026-06-03T20:47:45] Done (elapsed time=00:11:58, CPU time=00:11:58, peak memory=16gb)