[2026-06-08T08:43:07] Launching Arriba 2.4.0
[2026-06-08T08:43:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:27] Reading chimeric alignments from 'aih-tih-sc-6e7384-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=9623848)
[2026-06-08T08:52:01] Marking multi-mapping alignments (marked=5822910)
[2026-06-08T08:52:05] Detecting strandedness (reverse)
[2026-06-08T08:52:05] Assigning strands to alignments 
[2026-06-08T08:52:07] Annotating alignments 
[2026-06-08T08:52:41] Filtering duplicates (remaining=5859127)
[2026-06-08T08:52:48] 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=5635812)
[2026-06-08T08:52:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5635812)
[2026-06-08T08:52:51] Filtering viral contigs with expression lower than the top 5 (remaining=5635812)
[2026-06-08T08:52:56] Filtering viral contigs with less than 5% coverage (remaining=5635812)
[2026-06-08T08:52:58] Estimating fragment length (mate gap mean=-85.797, mate gap stddev=29.4245, read length mean=134.444)
[2026-06-08T08:52:58] Filtering read-through fragments with a distance <=10000bp (remaining=5348900)
[2026-06-08T08:53:00] Filtering inconsistently clipped mates (remaining=5292535)
[2026-06-08T08:53:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5185761)
[2026-06-08T08:53:07] Filtering fragments with small insert size (remaining=5185234)
[2026-06-08T08:53:09] Filtering alignments with long gaps (remaining=5185234)
[2026-06-08T08:53:11] Filtering fragments with both mates in the same gene (remaining=5183982)
[2026-06-08T08:53:14] Filtering fusions arising from hairpin structures (remaining=5010244)
[2026-06-08T08:53:16] Filtering reads with a mismatch p-value <=0.01 (remaining=2576356)
[2026-06-08T08:53:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=880395)
[2026-06-08T08:53:41] Finding fusions and counting supporting reads (total=564802)
[2026-06-08T08:53:58] Merging adjacent fusion breakpoints (remaining=559601)
[2026-06-08T08:53:59] Filtering multi-mapping fusions by alignment score and read support (remaining=372856)
[2026-06-08T08:54:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=371277)
[2026-06-08T08:54:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=225365)
[2026-06-08T08:54:39] Filtering fusions with <2 supporting reads (remaining=38065)
[2026-06-08T08:54:40] Filtering fusions with an e-value >=0.3 (remaining=12739)
[2026-06-08T08:54:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12774)
[2026-06-08T08:54:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12714)
[2026-06-08T08:54:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12714)
[2026-06-08T08:54:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8215)
[2026-06-08T08:54:51] Searching for fusions with spliced split reads (remaining=8348)
[2026-06-08T08:54:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=4892)
[2026-06-08T08:54:57] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4840)
[2026-06-08T08:54:57] Searching for fusions with >=4 spliced events (remaining=5569)
[2026-06-08T08:54:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1732)
[2026-06-08T08:55:16] Filtering fusions with anchors <=23nt (remaining=1409)
[2026-06-08T08:55:17] Filtering end-to-end fusions with low support (remaining=1381)
[2026-06-08T08:55:18] Filtering fusions with no coverage around the breakpoints (remaining=1342)
[2026-06-08T08:55:18] Indexing gene sequences 
[2026-06-08T08:55:25] Filtering genes with >=30% identity (remaining=426)
[2026-06-08T08:55:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=233)
[2026-06-08T08:55:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=209)
[2026-06-08T08:55:38] Searching for additional isoforms (remaining=274)
[2026-06-08T08:55:39] Assigning confidence scores to events 
[2026-06-08T08:55:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:42] Writing fusions to file 'aih-tih-sc-6e7384-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:44] Writing discarded fusions to file 'aih-tih-sc-6e7384-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:16] Freeing resources
[2026-06-08T08:56:39] Done (elapsed time=00:13:32, CPU time=00:13:31, peak memory=13.8gb)