[2026-06-03T19:52:40] Launching Arriba 2.4.0
[2026-06-03T19:52:40] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:52:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:52:54] Reading chimeric alignments from 'aih-tih-sc-8c7069-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9955194)
[2026-06-03T20:00:05] Marking multi-mapping alignments (marked=6987934)
[2026-06-03T20:00:11] Detecting strandedness (no)
[2026-06-03T20:00:11] Annotating alignments 
[2026-06-03T20:01:15] Filtering duplicates (remaining=4963492)
[2026-06-03T20:01:23] 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=4556120)
[2026-06-03T20:01:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4556120)
[2026-06-03T20:01:29] Filtering viral contigs with expression lower than the top 5 (remaining=4556120)
[2026-06-03T20:01:35] Filtering viral contigs with less than 5% coverage (remaining=4556120)
[2026-06-03T20:01:39] Estimating fragment length (mate gap mean=-82.5999, mate gap stddev=27.9235, read length mean=118.08)
[2026-06-03T20:01:39] Filtering read-through fragments with a distance <=10000bp (remaining=4284861)
[2026-06-03T20:01:42] Filtering inconsistently clipped mates (remaining=4172682)
[2026-06-03T20:01:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4016011)
[2026-06-03T20:01:52] Filtering fragments with small insert size (remaining=4014726)
[2026-06-03T20:01:55] Filtering alignments with long gaps (remaining=4014726)
[2026-06-03T20:01:58] Filtering fragments with both mates in the same gene (remaining=4013582)
[2026-06-03T20:02:01] Filtering fusions arising from hairpin structures (remaining=3724671)
[2026-06-03T20:02:05] Filtering reads with a mismatch p-value <=0.01 (remaining=1390525)
[2026-06-03T20:02:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=680140)
[2026-06-03T20:02:28] Finding fusions and counting supporting reads (total=567991)
[2026-06-03T20:02:54] Merging adjacent fusion breakpoints (remaining=560803)
[2026-06-03T20:02:56] Filtering multi-mapping fusions by alignment score and read support (remaining=311871)
[2026-06-03T20:03:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:03:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=310217)
[2026-06-03T20:03:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=186190)
[2026-06-03T20:03:59] Filtering fusions with <2 supporting reads (remaining=17796)
[2026-06-03T20:04:00] Filtering fusions with an e-value >=0.3 (remaining=4040)
[2026-06-03T20:04:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4104)
[2026-06-03T20:04:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4019)
[2026-06-03T20:04:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4019)
[2026-06-03T20:04:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3943)
[2026-06-03T20:04:17] Searching for fusions with spliced split reads (remaining=4031)
[2026-06-03T20:04:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=2851)
[2026-06-03T20:04:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2811)
[2026-06-03T20:04:29] Searching for fusions with >=4 spliced events (remaining=3275)
[2026-06-03T20:04:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1391)
[2026-06-03T20:04:55] Filtering fusions with anchors <=23nt (remaining=1203)
[2026-06-03T20:04:55] Filtering end-to-end fusions with low support (remaining=1168)
[2026-06-03T20:04:56] Filtering fusions with no coverage around the breakpoints (remaining=1149)
[2026-06-03T20:04:57] Indexing gene sequences 
[2026-06-03T20:05:07] Filtering genes with >=30% identity (remaining=377)
[2026-06-03T20:05:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=205)
[2026-06-03T20:05:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-03T20:05:17] Searching for additional isoforms (remaining=220)
[2026-06-03T20:05:18] Assigning confidence scores to events 
[2026-06-03T20:05:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:05:24] Writing fusions to file 'aih-tih-sc-8c7069-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:05:27] Writing discarded fusions to file 'aih-tih-sc-8c7069-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:06:13] Freeing resources
[2026-06-03T20:06:36] Done (elapsed time=00:13:56, CPU time=00:13:55, peak memory=14.7gb)