[2026-06-03T20:21:30] Launching Arriba 2.4.0
[2026-06-03T20:21:30] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:21:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:21:48] Reading chimeric alignments from 'aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9729226)
[2026-06-03T20:28:05] Marking multi-mapping alignments (marked=6666696)
[2026-06-03T20:28:09] Detecting strandedness (reverse)
[2026-06-03T20:28:09] Assigning strands to alignments 
[2026-06-03T20:28:10] Annotating alignments 
[2026-06-03T20:28:38] Filtering duplicates (remaining=5037903)
[2026-06-03T20:28:42] 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=4683441)
[2026-06-03T20:28:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4683441)
[2026-06-03T20:28:46] Filtering viral contigs with expression lower than the top 5 (remaining=4683441)
[2026-06-03T20:28:49] Filtering viral contigs with less than 5% coverage (remaining=4683441)
[2026-06-03T20:28:51] Estimating fragment length (mate gap mean=-81.4416, mate gap stddev=28.2484, read length mean=118.503)
[2026-06-03T20:28:51] Filtering read-through fragments with a distance <=10000bp (remaining=4436195)
[2026-06-03T20:28:53] Filtering inconsistently clipped mates (remaining=4327258)
[2026-06-03T20:28:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4175587)
[2026-06-03T20:28:58] Filtering fragments with small insert size (remaining=4174316)
[2026-06-03T20:28:59] Filtering alignments with long gaps (remaining=4174314)
[2026-06-03T20:29:01] Filtering fragments with both mates in the same gene (remaining=4173145)
[2026-06-03T20:29:03] Filtering fusions arising from hairpin structures (remaining=3878742)
[2026-06-03T20:29:05] Filtering reads with a mismatch p-value <=0.01 (remaining=1504994)
[2026-06-03T20:29:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=683597)
[2026-06-03T20:29:22] Finding fusions and counting supporting reads (total=564623)
[2026-06-03T20:29:34] Merging adjacent fusion breakpoints (remaining=558864)
[2026-06-03T20:29:35] Filtering multi-mapping fusions by alignment score and read support (remaining=323381)
[2026-06-03T20:30:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:30:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=321960)
[2026-06-03T20:30:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=187853)
[2026-06-03T20:30:07] Filtering fusions with <2 supporting reads (remaining=18226)
[2026-06-03T20:30:07] Filtering fusions with an e-value >=0.3 (remaining=4184)
[2026-06-03T20:30:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4240)
[2026-06-03T20:30:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4130)
[2026-06-03T20:30:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4130)
[2026-06-03T20:30:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3990)
[2026-06-03T20:30:16] Searching for fusions with spliced split reads (remaining=4074)
[2026-06-03T20:30:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=2913)
[2026-06-03T20:30:21] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2883)
[2026-06-03T20:30:22] Searching for fusions with >=4 spliced events (remaining=3285)
[2026-06-03T20:30:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1207)
[2026-06-03T20:30:39] Filtering fusions with anchors <=23nt (remaining=1010)
[2026-06-03T20:30:39] Filtering end-to-end fusions with low support (remaining=976)
[2026-06-03T20:30:40] Filtering fusions with no coverage around the breakpoints (remaining=963)
[2026-06-03T20:30:40] Indexing gene sequences 
[2026-06-03T20:30:45] Filtering genes with >=30% identity (remaining=321)
[2026-06-03T20:30:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=173)
[2026-06-03T20:30:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=159)
[2026-06-03T20:30:51] Searching for additional isoforms (remaining=189)
[2026-06-03T20:30:52] Assigning confidence scores to events 
[2026-06-03T20:30:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:30:55] Writing fusions to file 'aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:30:56] Writing discarded fusions to file 'aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:31:19] Freeing resources
[2026-06-03T20:31:33] Done (elapsed time=00:10:03, CPU time=00:10:02, peak memory=14.3gb)