[2026-06-08T08:57:18] Launching Arriba 2.4.0
[2026-06-08T08:57:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:57:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:57:31] Reading chimeric alignments from 'aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11726538)
[2026-06-08T09:04:37] Marking multi-mapping alignments (marked=7901765)
[2026-06-08T09:04:43] Detecting strandedness (reverse)
[2026-06-08T09:04:43] Assigning strands to alignments 
[2026-06-08T09:04:45] Annotating alignments 
[2026-06-08T09:05:26] Filtering duplicates (remaining=5451432)
[2026-06-08T09:05:33] 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=4984337)
[2026-06-08T09:05:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4984337)
[2026-06-08T09:05:38] Filtering viral contigs with expression lower than the top 5 (remaining=4984337)
[2026-06-08T09:05:43] Filtering viral contigs with less than 5% coverage (remaining=4984337)
[2026-06-08T09:05:46] Estimating fragment length (mate gap mean=-86.2964, mate gap stddev=28.9639, read length mean=128.272)
[2026-06-08T09:05:46] Filtering read-through fragments with a distance <=10000bp (remaining=4730600)
[2026-06-08T09:05:48] Filtering inconsistently clipped mates (remaining=4644708)
[2026-06-08T09:05:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4526594)
[2026-06-08T09:05:55] Filtering fragments with small insert size (remaining=4525815)
[2026-06-08T09:05:57] Filtering alignments with long gaps (remaining=4525815)
[2026-06-08T09:06:00] Filtering fragments with both mates in the same gene (remaining=4524969)
[2026-06-08T09:06:02] Filtering fusions arising from hairpin structures (remaining=4277940)
[2026-06-08T09:06:05] Filtering reads with a mismatch p-value <=0.01 (remaining=1904704)
[2026-06-08T09:06:17] Filtering reads with low entropy (k-mer content >=60%) (remaining=663405)
[2026-06-08T09:06:26] Finding fusions and counting supporting reads (total=534101)
[2026-06-08T09:06:44] Merging adjacent fusion breakpoints (remaining=529229)
[2026-06-08T09:06:46] Filtering multi-mapping fusions by alignment score and read support (remaining=323380)
[2026-06-08T09:07:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:07:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=321735)
[2026-06-08T09:07:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=176476)
[2026-06-08T09:07:31] Filtering fusions with <2 supporting reads (remaining=22460)
[2026-06-08T09:07:32] Filtering fusions with an e-value >=0.3 (remaining=7907)
[2026-06-08T09:07:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7946)
[2026-06-08T09:07:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7882)
[2026-06-08T09:07:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7882)
[2026-06-08T09:07:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4513)
[2026-06-08T09:07:43] Searching for fusions with spliced split reads (remaining=4605)
[2026-06-08T09:07:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=3142)
[2026-06-08T09:07:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3093)
[2026-06-08T09:07:50] Searching for fusions with >=4 spliced events (remaining=3627)
[2026-06-08T09:07:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1482)
[2026-06-08T09:08:05] Filtering fusions with anchors <=23nt (remaining=1171)
[2026-06-08T09:08:05] Filtering end-to-end fusions with low support (remaining=1112)
[2026-06-08T09:08:06] Filtering fusions with no coverage around the breakpoints (remaining=1088)
[2026-06-08T09:08:07] Indexing gene sequences 
[2026-06-08T09:08:11] Filtering genes with >=30% identity (remaining=364)
[2026-06-08T09:08:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=183)
[2026-06-08T09:08:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=182)
[2026-06-08T09:08:16] Searching for additional isoforms (remaining=206)
[2026-06-08T09:08:17] Assigning confidence scores to events 
[2026-06-08T09:08:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:08:20] Writing fusions to file 'aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:08:22] Writing discarded fusions to file 'aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:08:47] Freeing resources
[2026-06-08T09:09:05] Done (elapsed time=00:11:47, CPU time=00:11:45, peak memory=16.4gb)