[2026-06-03T19:13:56] Launching Arriba 2.4.0
[2026-06-03T19:13:56] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:14:12] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:14:19] Reading chimeric alignments from 'aih-tih-sc-598a93-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=3890264)
[2026-06-03T19:16:41] Marking multi-mapping alignments (marked=2967005)
[2026-06-03T19:16:42] Detecting strandedness (reverse)
[2026-06-03T19:16:42] Assigning strands to alignments 
[2026-06-03T19:16:43] Annotating alignments 
[2026-06-03T19:16:58] Filtering duplicates (remaining=1289562)
[2026-06-03T19:17:00] 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=1075021)
[2026-06-03T19:17:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1075021)
[2026-06-03T19:17:02] Filtering viral contigs with expression lower than the top 5 (remaining=1075021)
[2026-06-03T19:17:03] Filtering viral contigs with less than 5% coverage (remaining=1075021)
[2026-06-03T19:17:04] Estimating fragment length (mate gap mean=-76.6866, mate gap stddev=28.3748, read length mean=110.235)
[2026-06-03T19:17:04] Filtering read-through fragments with a distance <=10000bp (remaining=1036810)
[2026-06-03T19:17:05] Filtering inconsistently clipped mates (remaining=1003092)
[2026-06-03T19:17:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=952311)
[2026-06-03T19:17:07] Filtering fragments with small insert size (remaining=951580)
[2026-06-03T19:17:08] Filtering alignments with long gaps (remaining=951580)
[2026-06-03T19:17:08] Filtering fragments with both mates in the same gene (remaining=951127)
[2026-06-03T19:17:09] Filtering fusions arising from hairpin structures (remaining=881175)
[2026-06-03T19:17:10] Filtering reads with a mismatch p-value <=0.01 (remaining=266403)
[2026-06-03T19:17:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=112109)
[2026-06-03T19:17:15] Finding fusions and counting supporting reads (total=106370)
[2026-06-03T19:17:21] Merging adjacent fusion breakpoints (remaining=105610)
[2026-06-03T19:17:21] Filtering multi-mapping fusions by alignment score and read support (remaining=49547)
[2026-06-03T19:17:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:17:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=48990)
[2026-06-03T19:17:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=30324)
[2026-06-03T19:17:37] Filtering fusions with <2 supporting reads (remaining=1680)
[2026-06-03T19:17:38] Filtering fusions with an e-value >=0.3 (remaining=551)
[2026-06-03T19:17:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=576)
[2026-06-03T19:17:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=541)
[2026-06-03T19:17:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=541)
[2026-06-03T19:17:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=532)
[2026-06-03T19:17:41] Searching for fusions with spliced split reads (remaining=565)
[2026-06-03T19:17:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=426)
[2026-06-03T19:17:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=416)
[2026-06-03T19:17:44] Searching for fusions with >=4 spliced events (remaining=434)
[2026-06-03T19:17:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=126)
[2026-06-03T19:18:03] Filtering fusions with anchors <=23nt (remaining=100)
[2026-06-03T19:18:04] Filtering end-to-end fusions with low support (remaining=98)
[2026-06-03T19:18:04] Filtering fusions with no coverage around the breakpoints (remaining=96)
[2026-06-03T19:18:04] Indexing gene sequences 
[2026-06-03T19:18:05] Filtering genes with >=30% identity (remaining=31)
[2026-06-03T19:18:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=16)
[2026-06-03T19:18:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=16)
[2026-06-03T19:18:06] Searching for additional isoforms (remaining=18)
[2026-06-03T19:18:06] Assigning confidence scores to events 
[2026-06-03T19:18:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:18:07] Writing fusions to file 'aih-tih-sc-598a93-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:18:07] Writing discarded fusions to file 'aih-tih-sc-598a93-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:18:17] Freeing resources
[2026-06-03T19:18:24] Done (elapsed time=00:04:28, CPU time=00:04:26, peak memory=8.14gb)