[2026-06-03T20:11:22] Launching Arriba 2.4.0
[2026-06-03T20:11:22] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:11:31] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:11:35] Reading chimeric alignments from 'aih-tih-sc-56cab8-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10485731)
[2026-06-03T20:18:27] Marking multi-mapping alignments (marked=7075278)
[2026-06-03T20:18:31] Detecting strandedness (reverse)
[2026-06-03T20:18:31] Assigning strands to alignments 
[2026-06-03T20:18:33] Annotating alignments 
[2026-06-03T20:19:04] Filtering duplicates (remaining=6943379)
[2026-06-03T20:19:11] 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=6529431)
[2026-06-03T20:19:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6529431)
[2026-06-03T20:19:15] Filtering viral contigs with expression lower than the top 5 (remaining=6529431)
[2026-06-03T20:19:20] Filtering viral contigs with less than 5% coverage (remaining=6529431)
[2026-06-03T20:19:22] Estimating fragment length (mate gap mean=-85.6164, mate gap stddev=29.0944, read length mean=128.755)
[2026-06-03T20:19:22] Filtering read-through fragments with a distance <=10000bp (remaining=6135423)
[2026-06-03T20:19:24] Filtering inconsistently clipped mates (remaining=6015077)
[2026-06-03T20:19:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5844969)
[2026-06-03T20:19:31] Filtering fragments with small insert size (remaining=5844104)
[2026-06-03T20:19:33] Filtering alignments with long gaps (remaining=5844103)
[2026-06-03T20:19:35] Filtering fragments with both mates in the same gene (remaining=5842980)
[2026-06-03T20:19:37] Filtering fusions arising from hairpin structures (remaining=5435754)
[2026-06-03T20:19:39] Filtering reads with a mismatch p-value <=0.01 (remaining=2300811)
[2026-06-03T20:19:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=1107121)
[2026-06-03T20:20:02] Finding fusions and counting supporting reads (total=869585)
[2026-06-03T20:20:18] Merging adjacent fusion breakpoints (remaining=860729)
[2026-06-03T20:20:20] Filtering multi-mapping fusions by alignment score and read support (remaining=522305)
[2026-06-03T20:20:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:20:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=519894)
[2026-06-03T20:20:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=320918)
[2026-06-03T20:21:00] Filtering fusions with <2 supporting reads (remaining=33506)
[2026-06-03T20:21:01] Filtering fusions with an e-value >=0.3 (remaining=8049)
[2026-06-03T20:21:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8107)
[2026-06-03T20:21:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7995)
[2026-06-03T20:21:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7995)
[2026-06-03T20:21:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6542)
[2026-06-03T20:21:13] Searching for fusions with spliced split reads (remaining=6668)
[2026-06-03T20:21:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=4388)
[2026-06-03T20:21:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4360)
[2026-06-03T20:21:21] Searching for fusions with >=4 spliced events (remaining=5403)
[2026-06-03T20:21:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2293)
[2026-06-03T20:21:38] Filtering fusions with anchors <=23nt (remaining=1833)
[2026-06-03T20:21:39] Filtering end-to-end fusions with low support (remaining=1776)
[2026-06-03T20:21:40] Filtering fusions with no coverage around the breakpoints (remaining=1731)
[2026-06-03T20:21:41] Indexing gene sequences 
[2026-06-03T20:21:47] Filtering genes with >=30% identity (remaining=526)
[2026-06-03T20:21:49] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=200)
[2026-06-03T20:21:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=168)
[2026-06-03T20:21:54] Searching for additional isoforms (remaining=241)
[2026-06-03T20:21:55] Assigning confidence scores to events 
[2026-06-03T20:21:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:21:59] Writing fusions to file 'aih-tih-sc-56cab8-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:22:01] Writing discarded fusions to file 'aih-tih-sc-56cab8-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:22:30] Freeing resources
[2026-06-03T20:22:46] Done (elapsed time=00:11:24, CPU time=00:11:23, peak memory=15.4gb)