[2026-06-08T08:44:04] Launching Arriba 2.4.0
[2026-06-08T08:44:04] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:44:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:44:23] Reading chimeric alignments from 'aih-tih-sc-79f487-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10673203)
[2026-06-08T08:52:14] Marking multi-mapping alignments (marked=6934838)
[2026-06-08T08:52:18] Detecting strandedness (reverse)
[2026-06-08T08:52:18] Assigning strands to alignments 
[2026-06-08T08:52:20] Annotating alignments 
[2026-06-08T08:52:54] Filtering duplicates (remaining=7160923)
[2026-06-08T08:53:02] 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=6935455)
[2026-06-08T08:53:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6935455)
[2026-06-08T08:53:06] Filtering viral contigs with expression lower than the top 5 (remaining=6935455)
[2026-06-08T08:53:11] Filtering viral contigs with less than 5% coverage (remaining=6935455)
[2026-06-08T08:53:13] Estimating fragment length (mate gap mean=-85.4221, mate gap stddev=30.0259, read length mean=137.394)
[2026-06-08T08:53:13] Filtering read-through fragments with a distance <=10000bp (remaining=6561867)
[2026-06-08T08:53:15] Filtering inconsistently clipped mates (remaining=6481684)
[2026-06-08T08:53:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6336664)
[2026-06-08T08:53:21] Filtering fragments with small insert size (remaining=6336253)
[2026-06-08T08:53:23] Filtering alignments with long gaps (remaining=6336251)
[2026-06-08T08:53:26] Filtering fragments with both mates in the same gene (remaining=6335312)
[2026-06-08T08:53:28] Filtering fusions arising from hairpin structures (remaining=6037297)
[2026-06-08T08:53:30] Filtering reads with a mismatch p-value <=0.01 (remaining=3003339)
[2026-06-08T08:53:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=996314)
[2026-06-08T08:53:59] Finding fusions and counting supporting reads (total=710160)
[2026-06-08T08:54:16] Merging adjacent fusion breakpoints (remaining=701413)
[2026-06-08T08:54:18] Filtering multi-mapping fusions by alignment score and read support (remaining=443841)
[2026-06-08T08:54:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=441481)
[2026-06-08T08:54:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=252331)
[2026-06-08T08:55:00] Filtering fusions with <2 supporting reads (remaining=31435)
[2026-06-08T08:55:01] Filtering fusions with an e-value >=0.3 (remaining=10436)
[2026-06-08T08:55:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10497)
[2026-06-08T08:55:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10404)
[2026-06-08T08:55:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10405)
[2026-06-08T08:55:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7094)
[2026-06-08T08:55:13] Searching for fusions with spliced split reads (remaining=7230)
[2026-06-08T08:55:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=4137)
[2026-06-08T08:55:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4088)
[2026-06-08T08:55:20] Searching for fusions with >=4 spliced events (remaining=4804)
[2026-06-08T08:55:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1814)
[2026-06-08T08:55:40] Filtering fusions with anchors <=23nt (remaining=1423)
[2026-06-08T08:55:41] Filtering end-to-end fusions with low support (remaining=1390)
[2026-06-08T08:55:41] Filtering fusions with no coverage around the breakpoints (remaining=1357)
[2026-06-08T08:55:42] Indexing gene sequences 
[2026-06-08T08:55:48] Filtering genes with >=30% identity (remaining=427)
[2026-06-08T08:55:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=187)
[2026-06-08T08:55:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=185)
[2026-06-08T08:55:56] Searching for additional isoforms (remaining=225)
[2026-06-08T08:55:58] Assigning confidence scores to events 
[2026-06-08T08:56:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:56:01] Writing fusions to file 'aih-tih-sc-79f487-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:56:03] Writing discarded fusions to file 'aih-tih-sc-79f487-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:35] Freeing resources
[2026-06-08T08:56:52] Done (elapsed time=00:12:48, CPU time=00:12:47, peak memory=15gb)