[2026-06-08T08:00:41] Launching Arriba 2.4.0
[2026-06-08T08:00:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:00:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:01:03] Reading chimeric alignments from 'aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=5437392)
[2026-06-08T08:04:59] Marking multi-mapping alignments (marked=3680865)
[2026-06-08T08:05:02] Detecting strandedness (reverse)
[2026-06-08T08:05:02] Assigning strands to alignments 
[2026-06-08T08:05:03] Annotating alignments 
[2026-06-08T08:05:20] Filtering duplicates (remaining=3073581)
[2026-06-08T08:05:23] 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=2935016)
[2026-06-08T08:05:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2935016)
[2026-06-08T08:05:25] Filtering viral contigs with expression lower than the top 5 (remaining=2935016)
[2026-06-08T08:05:27] Filtering viral contigs with less than 5% coverage (remaining=2935016)
[2026-06-08T08:05:29] Estimating fragment length (mate gap mean=-86.655, mate gap stddev=27.3296, read length mean=129.506)
[2026-06-08T08:05:29] Filtering read-through fragments with a distance <=10000bp (remaining=2792414)
[2026-06-08T08:05:30] Filtering inconsistently clipped mates (remaining=2740284)
[2026-06-08T08:05:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2675743)
[2026-06-08T08:05:33] Filtering fragments with small insert size (remaining=2675480)
[2026-06-08T08:05:34] Filtering alignments with long gaps (remaining=2675480)
[2026-06-08T08:05:35] Filtering fragments with both mates in the same gene (remaining=2674985)
[2026-06-08T08:05:36] Filtering fusions arising from hairpin structures (remaining=2536099)
[2026-06-08T08:05:37] Filtering reads with a mismatch p-value <=0.01 (remaining=1218473)
[2026-06-08T08:05:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=398507)
[2026-06-08T08:05:49] Finding fusions and counting supporting reads (total=299590)
[2026-06-08T08:05:57] Merging adjacent fusion breakpoints (remaining=296439)
[2026-06-08T08:05:58] Filtering multi-mapping fusions by alignment score and read support (remaining=160991)
[2026-06-08T08:06:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:06:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=160261)
[2026-06-08T08:06:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=93954)
[2026-06-08T08:06:17] Filtering fusions with <2 supporting reads (remaining=11231)
[2026-06-08T08:06:18] Filtering fusions with an e-value >=0.3 (remaining=3088)
[2026-06-08T08:06:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3151)
[2026-06-08T08:06:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3106)
[2026-06-08T08:06:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3106)
[2026-06-08T08:06:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3055)
[2026-06-08T08:06:23] Searching for fusions with spliced split reads (remaining=3102)
[2026-06-08T08:06:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=2241)
[2026-06-08T08:06:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2218)
[2026-06-08T08:06:26] Searching for fusions with >=4 spliced events (remaining=2473)
[2026-06-08T08:06:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=778)
[2026-06-08T08:06:42] Filtering fusions with anchors <=23nt (remaining=657)
[2026-06-08T08:06:42] Filtering end-to-end fusions with low support (remaining=645)
[2026-06-08T08:06:43] Filtering fusions with no coverage around the breakpoints (remaining=626)
[2026-06-08T08:06:43] Indexing gene sequences 
[2026-06-08T08:06:47] Filtering genes with >=30% identity (remaining=191)
[2026-06-08T08:06:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=83)
[2026-06-08T08:06:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=75)
[2026-06-08T08:06:49] Searching for additional isoforms (remaining=95)
[2026-06-08T08:06:50] Assigning confidence scores to events 
[2026-06-08T08:06:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:06:52] Writing fusions to file 'aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:06:52] Writing discarded fusions to file 'aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:07:07] Freeing resources
[2026-06-08T08:07:15] Done (elapsed time=00:06:34, CPU time=00:06:34, peak memory=9.66gb)