[2026-06-03T20:17:44] Launching Arriba 2.4.0
[2026-06-03T20:17:44] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:17:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:17:56] Reading chimeric alignments from 'aih-tih-sc-cece97-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=12969776)
[2026-06-03T20:25:04] Marking multi-mapping alignments (marked=9301125)
[2026-06-03T20:25:09] Detecting strandedness (reverse)
[2026-06-03T20:25:09] Assigning strands to alignments 
[2026-06-03T20:25:11] Annotating alignments 
[2026-06-03T20:25:51] Filtering duplicates (remaining=6417031)
[2026-06-03T20:25:59] 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=5871466)
[2026-06-03T20:26:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5871466)
[2026-06-03T20:26:04] Filtering viral contigs with expression lower than the top 5 (remaining=5871466)
[2026-06-03T20:26:09] Filtering viral contigs with less than 5% coverage (remaining=5871466)
[2026-06-03T20:26:12] Estimating fragment length (mate gap mean=-84.3229, mate gap stddev=27.6316, read length mean=122.97)
[2026-06-03T20:26:12] Filtering read-through fragments with a distance <=10000bp (remaining=5449811)
[2026-06-03T20:26:14] Filtering inconsistently clipped mates (remaining=5320457)
[2026-06-03T20:26:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5156465)
[2026-06-03T20:26:21] Filtering fragments with small insert size (remaining=5155383)
[2026-06-03T20:26:23] Filtering alignments with long gaps (remaining=5155382)
[2026-06-03T20:26:26] Filtering fragments with both mates in the same gene (remaining=5154250)
[2026-06-03T20:26:28] Filtering fusions arising from hairpin structures (remaining=4773560)
[2026-06-03T20:26:31] Filtering reads with a mismatch p-value <=0.01 (remaining=1901246)
[2026-06-03T20:26:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=901679)
[2026-06-03T20:26:53] Finding fusions and counting supporting reads (total=685652)
[2026-06-03T20:27:10] Merging adjacent fusion breakpoints (remaining=677077)
[2026-06-03T20:27:12] Filtering multi-mapping fusions by alignment score and read support (remaining=391767)
[2026-06-03T20:27:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:27:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=389587)
[2026-06-03T20:27:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=218625)
[2026-06-03T20:27:56] Filtering fusions with <2 supporting reads (remaining=23829)
[2026-06-03T20:27:57] Filtering fusions with an e-value >=0.3 (remaining=5875)
[2026-06-03T20:27:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5960)
[2026-06-03T20:28:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5841)
[2026-06-03T20:28:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5841)
[2026-06-03T20:28:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5544)
[2026-06-03T20:28:09] Searching for fusions with spliced split reads (remaining=5633)
[2026-06-03T20:28:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=3822)
[2026-06-03T20:28:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3787)
[2026-06-03T20:28:17] Searching for fusions with >=4 spliced events (remaining=4345)
[2026-06-03T20:28:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1559)
[2026-06-03T20:28:34] Filtering fusions with anchors <=23nt (remaining=1219)
[2026-06-03T20:28:35] Filtering end-to-end fusions with low support (remaining=1176)
[2026-06-03T20:28:35] Filtering fusions with no coverage around the breakpoints (remaining=1154)
[2026-06-03T20:28:36] Indexing gene sequences 
[2026-06-03T20:28:41] Filtering genes with >=30% identity (remaining=363)
[2026-06-03T20:28:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=172)
[2026-06-03T20:28:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=157)
[2026-06-03T20:28:46] Searching for additional isoforms (remaining=198)
[2026-06-03T20:28:48] Assigning confidence scores to events 
[2026-06-03T20:28:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:28:51] Writing fusions to file 'aih-tih-sc-cece97-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:28:52] Writing discarded fusions to file 'aih-tih-sc-cece97-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:29:18] Freeing resources
[2026-06-03T20:29:37] Done (elapsed time=00:11:53, CPU time=00:11:51, peak memory=17.8gb)