[2026-06-03T20:42:45] Launching Arriba 2.4.0
[2026-06-03T20:42:45] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:42:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:42:56] Reading chimeric alignments from 'aih-tih-sc-9e2647-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9705265)
[2026-06-03T20:49:30] Marking multi-mapping alignments (marked=6143720)
[2026-06-03T20:49:34] Detecting strandedness (reverse)
[2026-06-03T20:49:34] Assigning strands to alignments 
[2026-06-03T20:49:36] Annotating alignments 
[2026-06-03T20:50:04] Filtering duplicates (remaining=6903610)
[2026-06-03T20:50:11] 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=6517796)
[2026-06-03T20:50:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6517796)
[2026-06-03T20:50:14] Filtering viral contigs with expression lower than the top 5 (remaining=6517796)
[2026-06-03T20:50:19] Filtering viral contigs with less than 5% coverage (remaining=6517796)
[2026-06-03T20:50:21] Estimating fragment length (mate gap mean=-84.4025, mate gap stddev=29.9694, read length mean=133.001)
[2026-06-03T20:50:21] Filtering read-through fragments with a distance <=10000bp (remaining=6111026)
[2026-06-03T20:50:23] Filtering inconsistently clipped mates (remaining=6005649)
[2026-06-03T20:50:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5826773)
[2026-06-03T20:50:29] Filtering fragments with small insert size (remaining=5825944)
[2026-06-03T20:50:31] Filtering alignments with long gaps (remaining=5825944)
[2026-06-03T20:50:33] Filtering fragments with both mates in the same gene (remaining=5824767)
[2026-06-03T20:50:35] Filtering fusions arising from hairpin structures (remaining=5469213)
[2026-06-03T20:50:38] Filtering reads with a mismatch p-value <=0.01 (remaining=2614430)
[2026-06-03T20:50:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=1305103)
[2026-06-03T20:51:02] Finding fusions and counting supporting reads (total=982410)
[2026-06-03T20:51:18] Merging adjacent fusion breakpoints (remaining=975805)
[2026-06-03T20:51:20] Filtering multi-mapping fusions by alignment score and read support (remaining=633147)
[2026-06-03T20:51:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:51:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=630690)
[2026-06-03T20:51:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=374608)
[2026-06-03T20:51:57] Filtering fusions with <2 supporting reads (remaining=51793)
[2026-06-03T20:51:58] Filtering fusions with an e-value >=0.3 (remaining=21419)
[2026-06-03T20:51:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=21465)
[2026-06-03T20:52:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=21386)
[2026-06-03T20:52:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=21386)
[2026-06-03T20:52:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8712)
[2026-06-03T20:52:09] Searching for fusions with spliced split reads (remaining=8737)
[2026-06-03T20:52:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=4844)
[2026-06-03T20:52:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4795)
[2026-06-03T20:52:17] Searching for fusions with >=4 spliced events (remaining=5965)
[2026-06-03T20:52:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2290)
[2026-06-03T20:52:34] Filtering fusions with anchors <=23nt (remaining=1859)
[2026-06-03T20:52:34] Filtering end-to-end fusions with low support (remaining=1795)
[2026-06-03T20:52:35] Filtering fusions with no coverage around the breakpoints (remaining=1752)
[2026-06-03T20:52:36] Indexing gene sequences 
[2026-06-03T20:52:42] Filtering genes with >=30% identity (remaining=501)
[2026-06-03T20:52:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=239)
[2026-06-03T20:52:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=196)
[2026-06-03T20:52:50] Searching for additional isoforms (remaining=275)
[2026-06-03T20:52:51] Assigning confidence scores to events 
[2026-06-03T20:52:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:52:55] Writing fusions to file 'aih-tih-sc-9e2647-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:52:58] Writing discarded fusions to file 'aih-tih-sc-9e2647-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:53:24] Freeing resources
[2026-06-03T20:53:40] Done (elapsed time=00:10:55, CPU time=00:10:55, peak memory=14.6gb)