[2026-06-08T08:53:09] Launching Arriba 2.4.0
[2026-06-08T08:53:09] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:21] Reading chimeric alignments from 'aih-tih-sc-a49d10-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12151398)
[2026-06-08T09:00:04] Marking multi-mapping alignments (marked=8111852)
[2026-06-08T09:00:08] Detecting strandedness (reverse)
[2026-06-08T09:00:08] Assigning strands to alignments 
[2026-06-08T09:00:11] Annotating alignments 
[2026-06-08T09:00:47] Filtering duplicates (remaining=7099683)
[2026-06-08T09:00:55] 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=6769383)
[2026-06-08T09:00:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6769383)
[2026-06-08T09:01:00] Filtering viral contigs with expression lower than the top 5 (remaining=6769383)
[2026-06-08T09:01:05] Filtering viral contigs with less than 5% coverage (remaining=6769383)
[2026-06-08T09:01:08] Estimating fragment length (mate gap mean=-86.9914, mate gap stddev=27.5244, read length mean=130.476)
[2026-06-08T09:01:08] Filtering read-through fragments with a distance <=10000bp (remaining=6470790)
[2026-06-08T09:01:10] Filtering inconsistently clipped mates (remaining=6368481)
[2026-06-08T09:01:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6218300)
[2026-06-08T09:01:16] Filtering fragments with small insert size (remaining=6217563)
[2026-06-08T09:01:18] Filtering alignments with long gaps (remaining=6217563)
[2026-06-08T09:01:21] Filtering fragments with both mates in the same gene (remaining=6216605)
[2026-06-08T09:01:23] Filtering fusions arising from hairpin structures (remaining=5937252)
[2026-06-08T09:01:26] Filtering reads with a mismatch p-value <=0.01 (remaining=2812150)
[2026-06-08T09:01:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=976087)
[2026-06-08T09:01:49] Finding fusions and counting supporting reads (total=680759)
[2026-06-08T09:02:05] Merging adjacent fusion breakpoints (remaining=672804)
[2026-06-08T09:02:07] Filtering multi-mapping fusions by alignment score and read support (remaining=387986)
[2026-06-08T09:02:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=385889)
[2026-06-08T09:02:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=239157)
[2026-06-08T09:02:49] Filtering fusions with <2 supporting reads (remaining=30115)
[2026-06-08T09:02:50] Filtering fusions with an e-value >=0.3 (remaining=7775)
[2026-06-08T09:02:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7831)
[2026-06-08T09:02:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7697)
[2026-06-08T09:02:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7697)
[2026-06-08T09:02:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7017)
[2026-06-08T09:03:02] Searching for fusions with spliced split reads (remaining=7028)
[2026-06-08T09:03:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=4354)
[2026-06-08T09:03:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4310)
[2026-06-08T09:03:10] Searching for fusions with >=4 spliced events (remaining=5182)
[2026-06-08T09:03:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2302)
[2026-06-08T09:03:27] Filtering fusions with anchors <=23nt (remaining=1956)
[2026-06-08T09:03:28] Filtering end-to-end fusions with low support (remaining=1913)
[2026-06-08T09:03:29] Filtering fusions with no coverage around the breakpoints (remaining=1883)
[2026-06-08T09:03:29] Indexing gene sequences 
[2026-06-08T09:03:37] Filtering genes with >=30% identity (remaining=680)
[2026-06-08T09:03:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=386)
[2026-06-08T09:03:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=284)
[2026-06-08T09:03:50] Searching for additional isoforms (remaining=361)
[2026-06-08T09:03:51] Assigning confidence scores to events 
[2026-06-08T09:03:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:55] Writing fusions to file 'aih-tih-sc-a49d10-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:58] Writing discarded fusions to file 'aih-tih-sc-a49d10-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:24] Freeing resources
[2026-06-08T09:04:42] Done (elapsed time=00:11:33, CPU time=00:11:31, peak memory=16.5gb)