[2026-06-08T08:48:23] Launching Arriba 2.4.0
[2026-06-08T08:48:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:37] Reading chimeric alignments from 'aih-tih-sc-ce6733-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12781285)
[2026-06-08T08:55:48] Marking multi-mapping alignments (marked=8538266)
[2026-06-08T08:55:53] Detecting strandedness (reverse)
[2026-06-08T08:55:53] Assigning strands to alignments 
[2026-06-08T08:55:56] Annotating alignments 
[2026-06-08T08:56:37] Filtering duplicates (remaining=7268364)
[2026-06-08T08:56:46] 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=6878693)
[2026-06-08T08:56:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6878693)
[2026-06-08T08:56:51] Filtering viral contigs with expression lower than the top 5 (remaining=6878693)
[2026-06-08T08:56:57] Filtering viral contigs with less than 5% coverage (remaining=6878693)
[2026-06-08T08:57:00] Estimating fragment length (mate gap mean=-86.3099, mate gap stddev=28.4384, read length mean=132.022)
[2026-06-08T08:57:00] Filtering read-through fragments with a distance <=10000bp (remaining=6534864)
[2026-06-08T08:57:03] Filtering inconsistently clipped mates (remaining=6435582)
[2026-06-08T08:57:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6286531)
[2026-06-08T08:57:10] Filtering fragments with small insert size (remaining=6285692)
[2026-06-08T08:57:13] Filtering alignments with long gaps (remaining=6285692)
[2026-06-08T08:57:15] Filtering fragments with both mates in the same gene (remaining=6284746)
[2026-06-08T08:57:18] Filtering fusions arising from hairpin structures (remaining=5941876)
[2026-06-08T08:57:21] Filtering reads with a mismatch p-value <=0.01 (remaining=2825869)
[2026-06-08T08:57:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=917448)
[2026-06-08T08:57:48] Finding fusions and counting supporting reads (total=654182)
[2026-06-08T08:58:07] Merging adjacent fusion breakpoints (remaining=646268)
[2026-06-08T08:58:09] Filtering multi-mapping fusions by alignment score and read support (remaining=398493)
[2026-06-08T08:58:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=396184)
[2026-06-08T08:58:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=220272)
[2026-06-08T08:58:59] Filtering fusions with <2 supporting reads (remaining=29119)
[2026-06-08T08:59:00] Filtering fusions with an e-value >=0.3 (remaining=8945)
[2026-06-08T08:59:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8997)
[2026-06-08T08:59:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8892)
[2026-06-08T08:59:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8892)
[2026-06-08T08:59:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6530)
[2026-06-08T08:59:13] Searching for fusions with spliced split reads (remaining=6642)
[2026-06-08T08:59:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=4230)
[2026-06-08T08:59:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4181)
[2026-06-08T08:59:21] Searching for fusions with >=4 spliced events (remaining=4900)
[2026-06-08T08:59:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1890)
[2026-06-08T08:59:39] Filtering fusions with anchors <=23nt (remaining=1535)
[2026-06-08T08:59:40] Filtering end-to-end fusions with low support (remaining=1495)
[2026-06-08T08:59:40] Filtering fusions with no coverage around the breakpoints (remaining=1456)
[2026-06-08T08:59:41] Indexing gene sequences 
[2026-06-08T08:59:48] Filtering genes with >=30% identity (remaining=557)
[2026-06-08T08:59:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=308)
[2026-06-08T08:59:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=243)
[2026-06-08T08:59:57] Searching for additional isoforms (remaining=303)
[2026-06-08T08:59:58] Assigning confidence scores to events 
[2026-06-08T09:00:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:02] Writing fusions to file 'aih-tih-sc-ce6733-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:04] Writing discarded fusions to file 'aih-tih-sc-ce6733-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:34] Freeing resources
[2026-06-08T09:00:54] Done (elapsed time=00:12:31, CPU time=00:12:30, peak memory=17.2gb)