[2026-06-08T08:42:20] Launching Arriba 2.4.0
[2026-06-08T08:42:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:33] Reading chimeric alignments from 'aih-tih-sc-33eb27-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11771937)
[2026-06-08T08:49:09] Marking multi-mapping alignments (marked=8093008)
[2026-06-08T08:49:13] Detecting strandedness (reverse)
[2026-06-08T08:49:13] Assigning strands to alignments 
[2026-06-08T08:49:16] Annotating alignments 
[2026-06-08T08:49:53] Filtering duplicates (remaining=5119256)
[2026-06-08T08:49:58] 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=4804401)
[2026-06-08T08:50:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4804401)
[2026-06-08T08:50:03] Filtering viral contigs with expression lower than the top 5 (remaining=4804401)
[2026-06-08T08:50:07] Filtering viral contigs with less than 5% coverage (remaining=4804401)
[2026-06-08T08:50:10] Estimating fragment length (mate gap mean=-84.4963, mate gap stddev=27.2572, read length mean=120.22)
[2026-06-08T08:50:10] Filtering read-through fragments with a distance <=10000bp (remaining=4475961)
[2026-06-08T08:50:12] Filtering inconsistently clipped mates (remaining=4390095)
[2026-06-08T08:50:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4300651)
[2026-06-08T08:50:18] Filtering fragments with small insert size (remaining=4299705)
[2026-06-08T08:50:20] Filtering alignments with long gaps (remaining=4299705)
[2026-06-08T08:50:22] Filtering fragments with both mates in the same gene (remaining=4298907)
[2026-06-08T08:50:25] Filtering fusions arising from hairpin structures (remaining=4068547)
[2026-06-08T08:50:27] Filtering reads with a mismatch p-value <=0.01 (remaining=1639074)
[2026-06-08T08:50:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=684493)
[2026-06-08T08:50:47] Finding fusions and counting supporting reads (total=575115)
[2026-06-08T08:51:03] Merging adjacent fusion breakpoints (remaining=566920)
[2026-06-08T08:51:05] Filtering multi-mapping fusions by alignment score and read support (remaining=334644)
[2026-06-08T08:51:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=333665)
[2026-06-08T08:51:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=183181)
[2026-06-08T08:51:49] Filtering fusions with <2 supporting reads (remaining=19781)
[2026-06-08T08:51:50] Filtering fusions with an e-value >=0.3 (remaining=4481)
[2026-06-08T08:51:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4522)
[2026-06-08T08:51:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4433)
[2026-06-08T08:51:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4433)
[2026-06-08T08:51:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4358)
[2026-06-08T08:52:01] Searching for fusions with spliced split reads (remaining=4422)
[2026-06-08T08:52:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=3089)
[2026-06-08T08:52:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3069)
[2026-06-08T08:52:07] Searching for fusions with >=4 spliced events (remaining=3698)
[2026-06-08T08:52:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1649)
[2026-06-08T08:52:23] Filtering fusions with anchors <=23nt (remaining=1370)
[2026-06-08T08:52:23] Filtering end-to-end fusions with low support (remaining=1326)
[2026-06-08T08:52:24] Filtering fusions with no coverage around the breakpoints (remaining=1301)
[2026-06-08T08:52:25] Indexing gene sequences 
[2026-06-08T08:52:31] Filtering genes with >=30% identity (remaining=414)
[2026-06-08T08:52:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=108)
[2026-06-08T08:52:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=108)
[2026-06-08T08:52:35] Searching for additional isoforms (remaining=130)
[2026-06-08T08:52:37] Assigning confidence scores to events 
[2026-06-08T08:52:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:40] Writing fusions to file 'aih-tih-sc-33eb27-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:52:41] Writing discarded fusions to file 'aih-tih-sc-33eb27-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:06] Freeing resources
[2026-06-08T08:53:23] Done (elapsed time=00:11:03, CPU time=00:11:02, peak memory=16.3gb)