[2026-06-08T08:28:59] Launching Arriba 2.4.0
[2026-06-08T08:28:59] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:29:12] Reading chimeric alignments from 'aih-tih-sc-d45d48-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8739315)
[2026-06-08T08:33:33] Marking multi-mapping alignments (marked=6411340)
[2026-06-08T08:33:37] Detecting strandedness (reverse)
[2026-06-08T08:33:37] Assigning strands to alignments 
[2026-06-08T08:33:39] Annotating alignments 
[2026-06-08T08:34:16] Filtering duplicates (remaining=2613567)
[2026-06-08T08:34:22] 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=2305726)
[2026-06-08T08:34:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2305726)
[2026-06-08T08:34:27] Filtering viral contigs with expression lower than the top 5 (remaining=2305726)
[2026-06-08T08:34:32] Filtering viral contigs with less than 5% coverage (remaining=2305726)
[2026-06-08T08:34:35] Estimating fragment length (mate gap mean=-85.1772, mate gap stddev=29.5828, read length mean=125.47)
[2026-06-08T08:34:35] Filtering read-through fragments with a distance <=10000bp (remaining=2217310)
[2026-06-08T08:34:37] Filtering inconsistently clipped mates (remaining=2172589)
[2026-06-08T08:34:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2094720)
[2026-06-08T08:34:43] Filtering fragments with small insert size (remaining=2094236)
[2026-06-08T08:34:46] Filtering alignments with long gaps (remaining=2094236)
[2026-06-08T08:34:48] Filtering fragments with both mates in the same gene (remaining=2093836)
[2026-06-08T08:34:51] Filtering fusions arising from hairpin structures (remaining=1981194)
[2026-06-08T08:34:53] Filtering reads with a mismatch p-value <=0.01 (remaining=827414)
[2026-06-08T08:35:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=235583)
[2026-06-08T08:35:09] Finding fusions and counting supporting reads (total=193806)
[2026-06-08T08:35:23] Merging adjacent fusion breakpoints (remaining=192612)
[2026-06-08T08:35:23] Filtering multi-mapping fusions by alignment score and read support (remaining=107098)
[2026-06-08T08:35:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=106000)
[2026-06-08T08:35:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=63009)
[2026-06-08T08:35:57] Filtering fusions with <2 supporting reads (remaining=5998)
[2026-06-08T08:35:58] Filtering fusions with an e-value >=0.3 (remaining=1946)
[2026-06-08T08:35:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1978)
[2026-06-08T08:36:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1923)
[2026-06-08T08:36:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1923)
[2026-06-08T08:36:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1623)
[2026-06-08T08:36:07] Searching for fusions with spliced split reads (remaining=1741)
[2026-06-08T08:36:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=1247)
[2026-06-08T08:36:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1227)
[2026-06-08T08:36:11] Searching for fusions with >=4 spliced events (remaining=1348)
[2026-06-08T08:36:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=442)
[2026-06-08T08:36:23] Filtering fusions with anchors <=23nt (remaining=349)
[2026-06-08T08:36:24] Filtering end-to-end fusions with low support (remaining=323)
[2026-06-08T08:36:24] Filtering fusions with no coverage around the breakpoints (remaining=314)
[2026-06-08T08:36:24] Indexing gene sequences 
[2026-06-08T08:36:26] Filtering genes with >=30% identity (remaining=138)
[2026-06-08T08:36:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=87)
[2026-06-08T08:36:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=73)
[2026-06-08T08:36:28] Searching for additional isoforms (remaining=86)
[2026-06-08T08:36:29] Assigning confidence scores to events 
[2026-06-08T08:36:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:30] Writing fusions to file 'aih-tih-sc-d45d48-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:36:31] Writing discarded fusions to file 'aih-tih-sc-d45d48-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:44] Freeing resources
[2026-06-08T08:36:56] Done (elapsed time=00:07:57, CPU time=00:07:56, peak memory=13.1gb)