[2026-06-08T08:52:08] Launching Arriba 2.4.0
[2026-06-08T08:52:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:27] Reading chimeric alignments from 'aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10730208)
[2026-06-08T09:00:52] Marking multi-mapping alignments (marked=6770235)
[2026-06-08T09:00:57] Detecting strandedness (reverse)
[2026-06-08T09:00:57] Assigning strands to alignments 
[2026-06-08T09:00:59] Annotating alignments 
[2026-06-08T09:01:34] Filtering duplicates (remaining=7132422)
[2026-06-08T09:01:41] 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=6867274)
[2026-06-08T09:01:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6867274)
[2026-06-08T09:01:46] Filtering viral contigs with expression lower than the top 5 (remaining=6867274)
[2026-06-08T09:01:51] Filtering viral contigs with less than 5% coverage (remaining=6867274)
[2026-06-08T09:01:53] Estimating fragment length (mate gap mean=-86.5866, mate gap stddev=29.5427, read length mean=134.444)
[2026-06-08T09:01:53] Filtering read-through fragments with a distance <=10000bp (remaining=6517347)
[2026-06-08T09:01:56] Filtering inconsistently clipped mates (remaining=6425137)
[2026-06-08T09:01:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6272735)
[2026-06-08T09:02:03] Filtering fragments with small insert size (remaining=6272038)
[2026-06-08T09:02:05] Filtering alignments with long gaps (remaining=6272038)
[2026-06-08T09:02:07] Filtering fragments with both mates in the same gene (remaining=6271026)
[2026-06-08T09:02:09] Filtering fusions arising from hairpin structures (remaining=5988095)
[2026-06-08T09:02:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2955452)
[2026-06-08T09:02:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=1024268)
[2026-06-08T09:02:40] Finding fusions and counting supporting reads (total=726980)
[2026-06-08T09:02:58] Merging adjacent fusion breakpoints (remaining=721459)
[2026-06-08T09:02:59] Filtering multi-mapping fusions by alignment score and read support (remaining=459409)
[2026-06-08T09:03:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=457214)
[2026-06-08T09:03:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=279141)
[2026-06-08T09:03:42] Filtering fusions with <2 supporting reads (remaining=32569)
[2026-06-08T09:03:43] Filtering fusions with an e-value >=0.3 (remaining=8686)
[2026-06-08T09:03:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8749)
[2026-06-08T09:03:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8679)
[2026-06-08T09:03:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8679)
[2026-06-08T09:03:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7654)
[2026-06-08T09:03:55] Searching for fusions with spliced split reads (remaining=7793)
[2026-06-08T09:04:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=4672)
[2026-06-08T09:04:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4606)
[2026-06-08T09:04:02] Searching for fusions with >=4 spliced events (remaining=5357)
[2026-06-08T09:04:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1992)
[2026-06-08T09:04:21] Filtering fusions with anchors <=23nt (remaining=1637)
[2026-06-08T09:04:22] Filtering end-to-end fusions with low support (remaining=1592)
[2026-06-08T09:04:23] Filtering fusions with no coverage around the breakpoints (remaining=1556)
[2026-06-08T09:04:24] Indexing gene sequences 
[2026-06-08T09:04:31] Filtering genes with >=30% identity (remaining=524)
[2026-06-08T09:04:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=244)
[2026-06-08T09:04:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=232)
[2026-06-08T09:04:44] Searching for additional isoforms (remaining=297)
[2026-06-08T09:04:45] Assigning confidence scores to events 
[2026-06-08T09:04:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:49] Writing fusions to file 'aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:04:51] Writing discarded fusions to file 'aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:23] Freeing resources
[2026-06-08T09:05:40] Done (elapsed time=00:13:32, CPU time=00:13:31, peak memory=15gb)