[2026-06-08T07:38:52] Launching Arriba 2.4.0
[2026-06-08T07:38:52] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:39:10] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:39:17] Reading chimeric alignments from 'aih-tih-sc-fba77b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=3636266)
[2026-06-08T07:41:51] Marking multi-mapping alignments (marked=2825216)
[2026-06-08T07:41:53] Detecting strandedness (no)
[2026-06-08T07:41:53] Annotating alignments 
[2026-06-08T07:42:12] Filtering duplicates (remaining=1172049)
[2026-06-08T07:42:15] 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=977240)
[2026-06-08T07:42:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=977240)
[2026-06-08T07:42:16] Filtering viral contigs with expression lower than the top 5 (remaining=977240)
[2026-06-08T07:42:18] Filtering viral contigs with less than 5% coverage (remaining=977240)
[2026-06-08T07:42:19] Estimating fragment length (mate gap mean=-70.2689, mate gap stddev=27.8809, read length mean=101.841)
[2026-06-08T07:42:19] Filtering read-through fragments with a distance <=10000bp (remaining=945417)
[2026-06-08T07:42:20] Filtering inconsistently clipped mates (remaining=912824)
[2026-06-08T07:42:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=858640)
[2026-06-08T07:42:22] Filtering fragments with small insert size (remaining=857931)
[2026-06-08T07:42:23] Filtering alignments with long gaps (remaining=857931)
[2026-06-08T07:42:23] Filtering fragments with both mates in the same gene (remaining=857422)
[2026-06-08T07:42:24] Filtering fusions arising from hairpin structures (remaining=797489)
[2026-06-08T07:42:25] Filtering reads with a mismatch p-value <=0.01 (remaining=215391)
[2026-06-08T07:42:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=90245)
[2026-06-08T07:42:30] Finding fusions and counting supporting reads (total=89086)
[2026-06-08T07:42:36] Merging adjacent fusion breakpoints (remaining=88467)
[2026-06-08T07:42:36] Filtering multi-mapping fusions by alignment score and read support (remaining=38824)
[2026-06-08T07:42:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:42:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=38384)
[2026-06-08T07:42:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=25679)
[2026-06-08T07:42:54] Filtering fusions with <2 supporting reads (remaining=1081)
[2026-06-08T07:42:54] Filtering fusions with an e-value >=0.3 (remaining=370)
[2026-06-08T07:42:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=392)
[2026-06-08T07:42:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=368)
[2026-06-08T07:42:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=368)
[2026-06-08T07:42:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=351)
[2026-06-08T07:42:58] Searching for fusions with spliced split reads (remaining=372)
[2026-06-08T07:43:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=285)
[2026-06-08T07:43:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=279)
[2026-06-08T07:43:00] Searching for fusions with >=4 spliced events (remaining=283)
[2026-06-08T07:43:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=81)
[2026-06-08T07:43:27] Filtering fusions with anchors <=23nt (remaining=66)
[2026-06-08T07:43:27] Filtering end-to-end fusions with low support (remaining=59)
[2026-06-08T07:43:27] Filtering fusions with no coverage around the breakpoints (remaining=56)
[2026-06-08T07:43:27] Indexing gene sequences 
[2026-06-08T07:43:28] Filtering genes with >=30% identity (remaining=15)
[2026-06-08T07:43:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=5)
[2026-06-08T07:43:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=5)
[2026-06-08T07:43:29] Searching for additional isoforms (remaining=9)
[2026-06-08T07:43:29] Assigning confidence scores to events 
[2026-06-08T07:43:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:43:31] Writing fusions to file 'aih-tih-sc-fba77b-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:43:31] Writing discarded fusions to file 'aih-tih-sc-fba77b-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:43:40] Freeing resources
[2026-06-08T07:43:49] Done (elapsed time=00:04:57, CPU time=00:04:55, peak memory=7.84gb)