[2026-06-08T08:57:17] Launching Arriba 2.4.0
[2026-06-08T08:57:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:57:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:57:33] Reading chimeric alignments from 'aih-tih-sc-13d441-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=8826267)
[2026-06-08T09:03:12] Marking multi-mapping alignments (marked=5692296)
[2026-06-08T09:03:15] Detecting strandedness (reverse)
[2026-06-08T09:03:15] Assigning strands to alignments 
[2026-06-08T09:03:17] Annotating alignments 
[2026-06-08T09:03:43] Filtering duplicates (remaining=5832060)
[2026-06-08T09:03:48] 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)
[2026-06-08T09:03:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5498904)
[2026-06-08T09:03:52] Filtering viral contigs with expression lower than the top 5 (remaining=5498904)
[2026-06-08T09:03:55] Filtering viral contigs with less than 5% coverage (remaining=5498904)
[2026-06-08T09:03:57] Estimating fragment length (mate gap mean=-85.2714, mate gap stddev=28.8927, read length mean=127.387)
[2026-06-08T09:03:57] Filtering read-through fragments with a distance <=10000bp (remaining=5120598)
[2026-06-08T09:03:59] Filtering inconsistently clipped mates (remaining=5014207)
[2026-06-08T09:04:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4866491)
[2026-06-08T09:04:04] Filtering fragments with small insert size (remaining=4865606)
[2026-06-08T09:04:05] Filtering alignments with long gaps (remaining=4865606)
[2026-06-08T09:04:07] Filtering fragments with both mates in the same gene (remaining=4864496)
[2026-06-08T09:04:08] Filtering fusions arising from hairpin structures (remaining=4540281)
[2026-06-08T09:04:10] Filtering reads with a mismatch p-value <=0.01 (remaining=1979551)
[2026-06-08T09:04:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=1010806)
[2026-06-08T09:04:31] Finding fusions and counting supporting reads (total=756681)
[2026-06-08T09:04:44] Merging adjacent fusion breakpoints (remaining=747561)
[2026-06-08T09:04:46] Filtering multi-mapping fusions by alignment score and read support (remaining=457807)
[2026-06-08T09:05:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:05:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=455736)
[2026-06-08T09:05:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=266188)
[2026-06-08T09:05:17] Filtering fusions with <2 supporting reads (remaining=34279)
[2026-06-08T09:05:17] Filtering fusions with an e-value >=0.3 (remaining=8748)
[2026-06-08T09:05:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8808)
[2026-06-08T09:05:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8701)
[2026-06-08T09:05:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8701)
[2026-06-08T09:05:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7999)
[2026-06-08T09:05:27] Searching for fusions with spliced split reads (remaining=8126)
[2026-06-08T09:05:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=5119)
[2026-06-08T09:05:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5066)
[2026-06-08T09:05:33] Searching for fusions with >=4 spliced events (remaining=5927)
[2026-06-08T09:05:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2019)
[2026-06-08T09:05:50] Filtering fusions with anchors <=23nt (remaining=1658)
[2026-06-08T09:05:50] Filtering end-to-end fusions with low support (remaining=1611)
[2026-06-08T09:05:51] Filtering fusions with no coverage around the breakpoints (remaining=1580)
[2026-06-08T09:05:51] Indexing gene sequences 
[2026-06-08T09:05:57] Filtering genes with >=30% identity (remaining=447)
[2026-06-08T09:06:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=179)
[2026-06-08T09:06:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-08T09:06:06] Searching for additional isoforms (remaining=214)
[2026-06-08T09:06:07] Assigning confidence scores to events 
[2026-06-08T09:06:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:06:09] Writing fusions to file 'aih-tih-sc-13d441-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:06:11] Writing discarded fusions to file 'aih-tih-sc-13d441-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:36] Freeing resources
[2026-06-08T09:06:50] Done (elapsed time=00:09:33, CPU time=00:09:32, peak memory=13.6gb)