[2026-06-08T08:55:08] Launching Arriba 2.4.0
[2026-06-08T08:55:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:55:22] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:55:27] Reading chimeric alignments from 'aih-tih-sc-934f55-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11828605)
[2026-06-08T09:03:52] Marking multi-mapping alignments (marked=7768048)
[2026-06-08T09:03:56] Detecting strandedness (reverse)
[2026-06-08T09:03:56] Assigning strands to alignments 
[2026-06-08T09:03:59] Annotating alignments 
[2026-06-08T09:04:34] Filtering duplicates (remaining=7654169)
[2026-06-08T09:04:42] 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=7350575)
[2026-06-08T09:04:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7350575)
[2026-06-08T09:04:47] Filtering viral contigs with expression lower than the top 5 (remaining=7350575)
[2026-06-08T09:04:52] Filtering viral contigs with less than 5% coverage (remaining=7350575)
[2026-06-08T09:04:54] Estimating fragment length (mate gap mean=-86.103, mate gap stddev=29.7824, read length mean=132.814)
[2026-06-08T09:04:55] Filtering read-through fragments with a distance <=10000bp (remaining=6901207)
[2026-06-08T09:04:57] Filtering inconsistently clipped mates (remaining=6807206)
[2026-06-08T09:04:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6678362)
[2026-06-08T09:05:04] Filtering fragments with small insert size (remaining=6677826)
[2026-06-08T09:05:06] Filtering alignments with long gaps (remaining=6677826)
[2026-06-08T09:05:09] Filtering fragments with both mates in the same gene (remaining=6676748)
[2026-06-08T09:05:11] Filtering fusions arising from hairpin structures (remaining=6357696)
[2026-06-08T09:05:14] Filtering reads with a mismatch p-value <=0.01 (remaining=3123506)
[2026-06-08T09:05:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=1083008)
[2026-06-08T09:05:44] Finding fusions and counting supporting reads (total=774969)
[2026-06-08T09:06:02] Merging adjacent fusion breakpoints (remaining=765640)
[2026-06-08T09:06:04] Filtering multi-mapping fusions by alignment score and read support (remaining=485786)
[2026-06-08T09:06:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:06:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=483861)
[2026-06-08T09:06:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=289598)
[2026-06-08T09:06:50] Filtering fusions with <2 supporting reads (remaining=34027)
[2026-06-08T09:06:51] Filtering fusions with an e-value >=0.3 (remaining=9295)
[2026-06-08T09:06:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9351)
[2026-06-08T09:06:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9277)
[2026-06-08T09:06:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9277)
[2026-06-08T09:06:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7518)
[2026-06-08T09:07:04] Searching for fusions with spliced split reads (remaining=7543)
[2026-06-08T09:07:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=4602)
[2026-06-08T09:07:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4550)
[2026-06-08T09:07:12] Searching for fusions with >=4 spliced events (remaining=5432)
[2026-06-08T09:07:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1999)
[2026-06-08T09:07:34] Filtering fusions with anchors <=23nt (remaining=1530)
[2026-06-08T09:07:35] Filtering end-to-end fusions with low support (remaining=1497)
[2026-06-08T09:07:35] Filtering fusions with no coverage around the breakpoints (remaining=1471)
[2026-06-08T09:07:36] Indexing gene sequences 
[2026-06-08T09:07:43] Filtering genes with >=30% identity (remaining=447)
[2026-06-08T09:07:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=228)
[2026-06-08T09:07:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=206)
[2026-06-08T09:07:52] Searching for additional isoforms (remaining=266)
[2026-06-08T09:07:54] Assigning confidence scores to events 
[2026-06-08T09:07:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:07:58] Writing fusions to file 'aih-tih-sc-934f55-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:08:00] Writing discarded fusions to file 'aih-tih-sc-934f55-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:08:37] Freeing resources
[2026-06-08T09:08:58] Done (elapsed time=00:13:50, CPU time=00:13:49, peak memory=16.2gb)