[2026-06-03T19:30:15] Launching Arriba 2.4.0
[2026-06-03T19:30:15] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:30:24] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:30:29] Reading chimeric alignments from 'aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=4370339)
[2026-06-03T19:34:28] Marking multi-mapping alignments (marked=2768819)
[2026-06-03T19:34:30] Detecting strandedness (reverse)
[2026-06-03T19:34:30] Assigning strands to alignments 
[2026-06-03T19:34:31] Annotating alignments 
[2026-06-03T19:34:49] Filtering duplicates (remaining=3372467)
[2026-06-03T19:34:53] 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=3238924)
[2026-06-03T19:34:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3238924)
[2026-06-03T19:34:55] Filtering viral contigs with expression lower than the top 5 (remaining=3238924)
[2026-06-03T19:34:57] Filtering viral contigs with less than 5% coverage (remaining=3238924)
[2026-06-03T19:34:59] Estimating fragment length (mate gap mean=-83.6262, mate gap stddev=29.7584, read length mean=132.16)
[2026-06-03T19:34:59] Filtering read-through fragments with a distance <=10000bp (remaining=3029527)
[2026-06-03T19:35:00] Filtering inconsistently clipped mates (remaining=2971698)
[2026-06-03T19:35:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2888482)
[2026-06-03T19:35:03] Filtering fragments with small insert size (remaining=2888019)
[2026-06-03T19:35:04] Filtering alignments with long gaps (remaining=2888018)
[2026-06-03T19:35:05] Filtering fragments with both mates in the same gene (remaining=2887431)
[2026-06-03T19:35:07] Filtering fusions arising from hairpin structures (remaining=2690895)
[2026-06-03T19:35:08] Filtering reads with a mismatch p-value <=0.01 (remaining=1335767)
[2026-06-03T19:35:17] Filtering reads with low entropy (k-mer content >=60%) (remaining=697689)
[2026-06-03T19:35:25] Finding fusions and counting supporting reads (total=549606)
[2026-06-03T19:35:35] Merging adjacent fusion breakpoints (remaining=545812)
[2026-06-03T19:35:36] Filtering multi-mapping fusions by alignment score and read support (remaining=340239)
[2026-06-03T19:35:56] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:36:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=338711)
[2026-06-03T19:36:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=198691)
[2026-06-03T19:36:03] Filtering fusions with <2 supporting reads (remaining=23432)
[2026-06-03T19:36:03] Filtering fusions with an e-value >=0.3 (remaining=6440)
[2026-06-03T19:36:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6496)
[2026-06-03T19:36:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6458)
[2026-06-03T19:36:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6458)
[2026-06-03T19:36:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5060)
[2026-06-03T19:36:10] Searching for fusions with spliced split reads (remaining=5197)
[2026-06-03T19:36:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=3282)
[2026-06-03T19:36:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3231)
[2026-06-03T19:36:15] Searching for fusions with >=4 spliced events (remaining=3726)
[2026-06-03T19:36:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1228)
[2026-06-03T19:36:34] Filtering fusions with anchors <=23nt (remaining=1035)
[2026-06-03T19:36:34] Filtering end-to-end fusions with low support (remaining=1014)
[2026-06-03T19:36:34] Filtering fusions with no coverage around the breakpoints (remaining=989)
[2026-06-03T19:36:35] Indexing gene sequences 
[2026-06-03T19:36:41] Filtering genes with >=30% identity (remaining=250)
[2026-06-03T19:36:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=115)
[2026-06-03T19:36:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=109)
[2026-06-03T19:36:47] Searching for additional isoforms (remaining=132)
[2026-06-03T19:36:48] Assigning confidence scores to events 
[2026-06-03T19:36:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:36:50] Writing fusions to file 'aih-tih-sc-3b436b-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:36:51] Writing discarded fusions to file 'aih-tih-sc-3b436b-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:37:13] Freeing resources
[2026-06-03T19:37:25] Done (elapsed time=00:07:10, CPU time=00:07:09, peak memory=8.81gb)