[2026-06-08T08:58:21] Launching Arriba 2.4.0
[2026-06-08T08:58:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:58:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:58:34] Reading chimeric alignments from 'aih-tih-sc-96af5b-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11158483)
[2026-06-08T09:05:50] Marking multi-mapping alignments (marked=7341076)
[2026-06-08T09:05:56] Detecting strandedness (reverse)
[2026-06-08T09:05:56] Assigning strands to alignments 
[2026-06-08T09:05:58] Annotating alignments 
[2026-06-08T09:06:40] Filtering duplicates (remaining=6321710)
[2026-06-08T09:06:49] 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=5994669)
[2026-06-08T09:06:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5994669)
[2026-06-08T09:06:54] Filtering viral contigs with expression lower than the top 5 (remaining=5994669)
[2026-06-08T09:07:00] Filtering viral contigs with less than 5% coverage (remaining=5994669)
[2026-06-08T09:07:03] Estimating fragment length (mate gap mean=-86.8321, mate gap stddev=28.0729, read length mean=127.111)
[2026-06-08T09:07:03] Filtering read-through fragments with a distance <=10000bp (remaining=5497994)
[2026-06-08T09:07:06] Filtering inconsistently clipped mates (remaining=5406573)
[2026-06-08T09:07:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5294729)
[2026-06-08T09:07:14] Filtering fragments with small insert size (remaining=5293910)
[2026-06-08T09:07:17] Filtering alignments with long gaps (remaining=5293910)
[2026-06-08T09:07:19] Filtering fragments with both mates in the same gene (remaining=5293024)
[2026-06-08T09:07:22] Filtering fusions arising from hairpin structures (remaining=5009558)
[2026-06-08T09:07:25] Filtering reads with a mismatch p-value <=0.01 (remaining=2150015)
[2026-06-08T09:07:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=1028602)
[2026-06-08T09:07:51] Finding fusions and counting supporting reads (total=818436)
[2026-06-08T09:08:11] Merging adjacent fusion breakpoints (remaining=808107)
[2026-06-08T09:08:13] Filtering multi-mapping fusions by alignment score and read support (remaining=486787)
[2026-06-08T09:08:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:08:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=485288)
[2026-06-08T09:09:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=256513)
[2026-06-08T09:09:01] Filtering fusions with <2 supporting reads (remaining=31061)
[2026-06-08T09:09:02] Filtering fusions with an e-value >=0.3 (remaining=7264)
[2026-06-08T09:09:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7309)
[2026-06-08T09:09:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7221)
[2026-06-08T09:09:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7221)
[2026-06-08T09:09:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6740)
[2026-06-08T09:09:14] Searching for fusions with spliced split reads (remaining=6828)
[2026-06-08T09:09:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=4396)
[2026-06-08T09:09:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4356)
[2026-06-08T09:09:21] Searching for fusions with >=4 spliced events (remaining=5406)
[2026-06-08T09:09:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2412)
[2026-06-08T09:09:40] Filtering fusions with anchors <=23nt (remaining=1894)
[2026-06-08T09:09:41] Filtering end-to-end fusions with low support (remaining=1829)
[2026-06-08T09:09:41] Filtering fusions with no coverage around the breakpoints (remaining=1788)
[2026-06-08T09:09:42] Indexing gene sequences 
[2026-06-08T09:09:48] Filtering genes with >=30% identity (remaining=438)
[2026-06-08T09:09:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=106)
[2026-06-08T09:09:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=102)
[2026-06-08T09:09:53] Searching for additional isoforms (remaining=139)
[2026-06-08T09:09:55] Assigning confidence scores to events 
[2026-06-08T09:09:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:09:58] Writing fusions to file 'aih-tih-sc-96af5b-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:10:00] Writing discarded fusions to file 'aih-tih-sc-96af5b-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:33] Freeing resources
[2026-06-08T09:10:52] Done (elapsed time=00:12:31, CPU time=00:12:30, peak memory=15.9gb)