[2026-06-08T08:41:58] Launching Arriba 2.4.0
[2026-06-08T08:41:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:15] Reading chimeric alignments from 'aih-tih-sc-0fc41c-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=9928905)
[2026-06-08T08:48:53] Marking multi-mapping alignments (marked=6761383)
[2026-06-08T08:48:57] Detecting strandedness (reverse)
[2026-06-08T08:48:57] Assigning strands to alignments 
[2026-06-08T08:48:59] Annotating alignments 
[2026-06-08T08:49:35] Filtering duplicates (remaining=5660332)
[2026-06-08T08:49:41] 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=5400861)
[2026-06-08T08:49:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5400861)
[2026-06-08T08:49:45] Filtering viral contigs with expression lower than the top 5 (remaining=5400861)
[2026-06-08T08:49:50] Filtering viral contigs with less than 5% coverage (remaining=5400861)
[2026-06-08T08:49:52] Estimating fragment length (mate gap mean=-85.1968, mate gap stddev=28.7713, read length mean=127.529)
[2026-06-08T08:49:52] Filtering read-through fragments with a distance <=10000bp (remaining=5084235)
[2026-06-08T08:49:54] Filtering inconsistently clipped mates (remaining=4992125)
[2026-06-08T08:49:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4871275)
[2026-06-08T08:50:00] Filtering fragments with small insert size (remaining=4870722)
[2026-06-08T08:50:03] Filtering alignments with long gaps (remaining=4870722)
[2026-06-08T08:50:05] Filtering fragments with both mates in the same gene (remaining=4869842)
[2026-06-08T08:50:08] Filtering fusions arising from hairpin structures (remaining=4604619)
[2026-06-08T08:50:11] Filtering reads with a mismatch p-value <=0.01 (remaining=2132998)
[2026-06-08T08:50:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=684121)
[2026-06-08T08:50:37] Finding fusions and counting supporting reads (total=520439)
[2026-06-08T08:50:53] Merging adjacent fusion breakpoints (remaining=512089)
[2026-06-08T08:50:54] Filtering multi-mapping fusions by alignment score and read support (remaining=301768)
[2026-06-08T08:51:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=300560)
[2026-06-08T08:51:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=165571)
[2026-06-08T08:51:36] Filtering fusions with <2 supporting reads (remaining=17169)
[2026-06-08T08:51:37] Filtering fusions with an e-value >=0.3 (remaining=4536)
[2026-06-08T08:51:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4599)
[2026-06-08T08:51:41] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4498)
[2026-06-08T08:51:42] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4500)
[2026-06-08T08:51:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4338)
[2026-06-08T08:51:48] Searching for fusions with spliced split reads (remaining=4419)
[2026-06-08T08:51:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=3018)
[2026-06-08T08:51:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2962)
[2026-06-08T08:51:54] Searching for fusions with >=4 spliced events (remaining=3343)
[2026-06-08T08:51:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1328)
[2026-06-08T08:52:13] Filtering fusions with anchors <=23nt (remaining=1043)
[2026-06-08T08:52:14] Filtering end-to-end fusions with low support (remaining=1015)
[2026-06-08T08:52:14] Filtering fusions with no coverage around the breakpoints (remaining=995)
[2026-06-08T08:52:15] Indexing gene sequences 
[2026-06-08T08:52:21] Filtering genes with >=30% identity (remaining=350)
[2026-06-08T08:52:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=177)
[2026-06-08T08:52:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=162)
[2026-06-08T08:52:30] Searching for additional isoforms (remaining=186)
[2026-06-08T08:52:31] Assigning confidence scores to events 
[2026-06-08T08:52:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:34] Writing fusions to file 'aih-tih-sc-0fc41c-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:52:36] Writing discarded fusions to file 'aih-tih-sc-0fc41c-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:08] Freeing resources
[2026-06-08T08:53:32] Done (elapsed time=00:11:34, CPU time=00:11:34, peak memory=14.2gb)