[2026-06-08T08:46:08] Launching Arriba 2.4.0
[2026-06-08T08:46:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:20] Reading chimeric alignments from 'aih-tih-sc-c63171-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12713110)
[2026-06-08T08:53:39] Marking multi-mapping alignments (marked=8668694)
[2026-06-08T08:53:44] Detecting strandedness (reverse)
[2026-06-08T08:53:44] Assigning strands to alignments 
[2026-06-08T08:53:47] Annotating alignments 
[2026-06-08T08:54:32] Filtering duplicates (remaining=7023125)
[2026-06-08T08:54:41] 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=6650675)
[2026-06-08T08:54:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6650675)
[2026-06-08T08:54:47] Filtering viral contigs with expression lower than the top 5 (remaining=6650675)
[2026-06-08T08:54:54] Filtering viral contigs with less than 5% coverage (remaining=6650675)
[2026-06-08T08:54:57] Estimating fragment length (mate gap mean=-85.8162, mate gap stddev=27.4607, read length mean=127.234)
[2026-06-08T08:54:57] Filtering read-through fragments with a distance <=10000bp (remaining=6290144)
[2026-06-08T08:55:00] Filtering inconsistently clipped mates (remaining=6185598)
[2026-06-08T08:55:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6023633)
[2026-06-08T08:55:08] Filtering fragments with small insert size (remaining=6022938)
[2026-06-08T08:55:11] Filtering alignments with long gaps (remaining=6022938)
[2026-06-08T08:55:14] Filtering fragments with both mates in the same gene (remaining=6021883)
[2026-06-08T08:55:17] Filtering fusions arising from hairpin structures (remaining=5712133)
[2026-06-08T08:55:20] Filtering reads with a mismatch p-value <=0.01 (remaining=2571997)
[2026-06-08T08:55:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=855095)
[2026-06-08T08:55:47] Finding fusions and counting supporting reads (total=641645)
[2026-06-08T08:56:09] Merging adjacent fusion breakpoints (remaining=633155)
[2026-06-08T08:56:11] Filtering multi-mapping fusions by alignment score and read support (remaining=373451)
[2026-06-08T08:56:56] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=372207)
[2026-06-08T08:57:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=215965)
[2026-06-08T08:57:07] Filtering fusions with <2 supporting reads (remaining=24026)
[2026-06-08T08:57:08] Filtering fusions with an e-value >=0.3 (remaining=5986)
[2026-06-08T08:57:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6053)
[2026-06-08T08:57:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5947)
[2026-06-08T08:57:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5947)
[2026-06-08T08:57:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5663)
[2026-06-08T08:57:23] Searching for fusions with spliced split reads (remaining=5752)
[2026-06-08T08:57:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=3926)
[2026-06-08T08:57:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3891)
[2026-06-08T08:57:32] Searching for fusions with >=4 spliced events (remaining=4580)
[2026-06-08T08:57:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1897)
[2026-06-08T08:57:53] Filtering fusions with anchors <=23nt (remaining=1439)
[2026-06-08T08:57:54] Filtering end-to-end fusions with low support (remaining=1403)
[2026-06-08T08:57:55] Filtering fusions with no coverage around the breakpoints (remaining=1357)
[2026-06-08T08:57:56] Indexing gene sequences 
[2026-06-08T08:58:01] Filtering genes with >=30% identity (remaining=419)
[2026-06-08T08:58:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=135)
[2026-06-08T08:58:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=124)
[2026-06-08T08:58:09] Searching for additional isoforms (remaining=161)
[2026-06-08T08:58:11] Assigning confidence scores to events 
[2026-06-08T08:58:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:15] Writing fusions to file 'aih-tih-sc-c63171-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:16] Writing discarded fusions to file 'aih-tih-sc-c63171-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:51] Freeing resources
[2026-06-08T08:59:11] Done (elapsed time=00:13:03, CPU time=00:13:02, peak memory=17.1gb)