[2026-06-08T08:29:07] Launching Arriba 2.4.0
[2026-06-08T08:29:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:29:22] Reading chimeric alignments from 'aih-tih-sc-ce4cdc-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8300292)
[2026-06-08T08:34:08] Marking multi-mapping alignments (marked=5252163)
[2026-06-08T08:34:11] Detecting strandedness (reverse)
[2026-06-08T08:34:11] Assigning strands to alignments 
[2026-06-08T08:34:12] Annotating alignments 
[2026-06-08T08:34:36] Filtering duplicates (remaining=3906730)
[2026-06-08T08:34:40] 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=3760784)
[2026-06-08T08:34:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3760784)
[2026-06-08T08:34:43] Filtering viral contigs with expression lower than the top 5 (remaining=3760784)
[2026-06-08T08:34:46] Filtering viral contigs with less than 5% coverage (remaining=3760784)
[2026-06-08T08:34:48] Estimating fragment length (mate gap mean=-86.8778, mate gap stddev=27.1105, read length mean=127.605)
[2026-06-08T08:34:48] Filtering read-through fragments with a distance <=10000bp (remaining=3506072)
[2026-06-08T08:34:50] Filtering inconsistently clipped mates (remaining=3443006)
[2026-06-08T08:34:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3352003)
[2026-06-08T08:34:54] Filtering fragments with small insert size (remaining=3351405)
[2026-06-08T08:34:55] Filtering alignments with long gaps (remaining=3351405)
[2026-06-08T08:34:57] Filtering fragments with both mates in the same gene (remaining=3350663)
[2026-06-08T08:34:58] Filtering fusions arising from hairpin structures (remaining=3174347)
[2026-06-08T08:35:00] Filtering reads with a mismatch p-value <=0.01 (remaining=1472017)
[2026-06-08T08:35:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=680723)
[2026-06-08T08:35:16] Finding fusions and counting supporting reads (total=547589)
[2026-06-08T08:35:27] Merging adjacent fusion breakpoints (remaining=542874)
[2026-06-08T08:35:28] Filtering multi-mapping fusions by alignment score and read support (remaining=312084)
[2026-06-08T08:35:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=310809)
[2026-06-08T08:35:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=171919)
[2026-06-08T08:35:55] Filtering fusions with <2 supporting reads (remaining=22457)
[2026-06-08T08:35:55] Filtering fusions with an e-value >=0.3 (remaining=5934)
[2026-06-08T08:35:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5983)
[2026-06-08T08:35:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5924)
[2026-06-08T08:35:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5924)
[2026-06-08T08:35:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5735)
[2026-06-08T08:36:03] Searching for fusions with spliced split reads (remaining=5796)
[2026-06-08T08:36:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=3869)
[2026-06-08T08:36:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3825)
[2026-06-08T08:36:07] Searching for fusions with >=4 spliced events (remaining=4405)
[2026-06-08T08:36:08] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1382)
[2026-06-08T08:36:21] Filtering fusions with anchors <=23nt (remaining=1196)
[2026-06-08T08:36:21] Filtering end-to-end fusions with low support (remaining=1163)
[2026-06-08T08:36:21] Filtering fusions with no coverage around the breakpoints (remaining=1138)
[2026-06-08T08:36:22] Indexing gene sequences 
[2026-06-08T08:36:26] Filtering genes with >=30% identity (remaining=359)
[2026-06-08T08:36:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=178)
[2026-06-08T08:36:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=156)
[2026-06-08T08:36:30] Searching for additional isoforms (remaining=184)
[2026-06-08T08:36:31] Assigning confidence scores to events 
[2026-06-08T08:36:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:33] Writing fusions to file 'aih-tih-sc-ce4cdc-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:36:35] Writing discarded fusions to file 'aih-tih-sc-ce4cdc-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:52] Freeing resources
[2026-06-08T08:37:05] Done (elapsed time=00:07:58, CPU time=00:07:57, peak memory=12.8gb)