[2026-06-08T08:44:30] Launching Arriba 2.4.0
[2026-06-08T08:44:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:44:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:44:42] Reading chimeric alignments from 'aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10008454)
[2026-06-08T08:51:29] Marking multi-mapping alignments (marked=6485681)
[2026-06-08T08:51:33] Detecting strandedness (no)
[2026-06-08T08:51:33] Annotating alignments 
[2026-06-08T08:52:16] Filtering duplicates (remaining=6688256)
[2026-06-08T08:52:24] 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=6294525)
[2026-06-08T08:52:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6294525)
[2026-06-08T08:52:28] Filtering viral contigs with expression lower than the top 5 (remaining=6294525)
[2026-06-08T08:52:33] Filtering viral contigs with less than 5% coverage (remaining=6294525)
[2026-06-08T08:52:36] Estimating fragment length (mate gap mean=-85.2079, mate gap stddev=28.9414, read length mean=127.085)
[2026-06-08T08:52:36] Filtering read-through fragments with a distance <=10000bp (remaining=5924740)
[2026-06-08T08:52:38] Filtering inconsistently clipped mates (remaining=5794806)
[2026-06-08T08:52:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5639024)
[2026-06-08T08:52:46] Filtering fragments with small insert size (remaining=5637965)
[2026-06-08T08:52:48] Filtering alignments with long gaps (remaining=5637965)
[2026-06-08T08:52:51] Filtering fragments with both mates in the same gene (remaining=5637032)
[2026-06-08T08:52:53] Filtering fusions arising from hairpin structures (remaining=5243578)
[2026-06-08T08:52:56] Filtering reads with a mismatch p-value <=0.01 (remaining=2182315)
[2026-06-08T08:53:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=1056725)
[2026-06-08T08:53:21] Finding fusions and counting supporting reads (total=820853)
[2026-06-08T08:53:38] Merging adjacent fusion breakpoints (remaining=811635)
[2026-06-08T08:53:40] Filtering multi-mapping fusions by alignment score and read support (remaining=516709)
[2026-06-08T08:54:17] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=514827)
[2026-06-08T08:54:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=308234)
[2026-06-08T08:54:27] Filtering fusions with <2 supporting reads (remaining=36184)
[2026-06-08T08:54:28] Filtering fusions with an e-value >=0.3 (remaining=9304)
[2026-06-08T08:54:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9366)
[2026-06-08T08:54:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9265)
[2026-06-08T08:54:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9265)
[2026-06-08T08:54:35] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6799)
[2026-06-08T08:54:41] Searching for fusions with spliced split reads (remaining=6936)
[2026-06-08T08:54:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=4634)
[2026-06-08T08:54:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4584)
[2026-06-08T08:54:49] Searching for fusions with >=4 spliced events (remaining=5451)
[2026-06-08T08:54:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2130)
[2026-06-08T08:55:06] Filtering fusions with anchors <=23nt (remaining=1701)
[2026-06-08T08:55:07] Filtering end-to-end fusions with low support (remaining=1650)
[2026-06-08T08:55:07] Filtering fusions with no coverage around the breakpoints (remaining=1615)
[2026-06-08T08:55:08] Indexing gene sequences 
[2026-06-08T08:55:15] Filtering genes with >=30% identity (remaining=567)
[2026-06-08T08:55:18] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=297)
[2026-06-08T08:55:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=239)
[2026-06-08T08:55:50] Searching for additional isoforms (remaining=316)
[2026-06-08T08:55:52] Assigning confidence scores to events 
[2026-06-08T08:55:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:55] Writing fusions to file 'aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:58] Writing discarded fusions to file 'aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:33] Freeing resources
[2026-06-08T08:56:51] Done (elapsed time=00:12:21, CPU time=00:12:21, peak memory=14.8gb)