[2026-06-08T08:35:07] Launching Arriba 2.4.0
[2026-06-08T08:35:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:22] Reading chimeric alignments from 'aih-tih-sc-00d05f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8576979)
[2026-06-08T08:41:26] Marking multi-mapping alignments (marked=5773248)
[2026-06-08T08:41:32] Detecting strandedness (reverse)
[2026-06-08T08:41:32] Assigning strands to alignments 
[2026-06-08T08:41:34] Annotating alignments 
[2026-06-08T08:42:17] Filtering duplicates (remaining=3552010)
[2026-06-08T08:42:26] 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=3290374)
[2026-06-08T08:42:29] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3290374)
[2026-06-08T08:42:32] Filtering viral contigs with expression lower than the top 5 (remaining=3290374)
[2026-06-08T08:42:37] Filtering viral contigs with less than 5% coverage (remaining=3290374)
[2026-06-08T08:42:40] Estimating fragment length (mate gap mean=-86.3951, mate gap stddev=29.1551, read length mean=129.888)
[2026-06-08T08:42:40] Filtering read-through fragments with a distance <=10000bp (remaining=3157532)
[2026-06-08T08:42:43] Filtering inconsistently clipped mates (remaining=3097593)
[2026-06-08T08:42:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2991481)
[2026-06-08T08:42:50] Filtering fragments with small insert size (remaining=2990978)
[2026-06-08T08:42:53] Filtering alignments with long gaps (remaining=2990978)
[2026-06-08T08:42:56] Filtering fragments with both mates in the same gene (remaining=2990363)
[2026-06-08T08:42:59] Filtering fusions arising from hairpin structures (remaining=2823949)
[2026-06-08T08:43:02] Filtering reads with a mismatch p-value <=0.01 (remaining=1199810)
[2026-06-08T08:43:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=404715)
[2026-06-08T08:43:20] Finding fusions and counting supporting reads (total=328915)
[2026-06-08T08:43:39] Merging adjacent fusion breakpoints (remaining=326493)
[2026-06-08T08:43:41] Filtering multi-mapping fusions by alignment score and read support (remaining=195214)
[2026-06-08T08:44:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=193030)
[2026-06-08T08:44:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=111969)
[2026-06-08T08:44:34] Filtering fusions with <2 supporting reads (remaining=13618)
[2026-06-08T08:44:35] Filtering fusions with an e-value >=0.3 (remaining=4192)
[2026-06-08T08:44:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4230)
[2026-06-08T08:44:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4176)
[2026-06-08T08:44:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4176)
[2026-06-08T08:44:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3167)
[2026-06-08T08:44:46] Searching for fusions with spliced split reads (remaining=3211)
[2026-06-08T08:44:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=2357)
[2026-06-08T08:44:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2321)
[2026-06-08T08:44:53] Searching for fusions with >=4 spliced events (remaining=2602)
[2026-06-08T08:44:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=778)
[2026-06-08T08:45:11] Filtering fusions with anchors <=23nt (remaining=638)
[2026-06-08T08:45:11] Filtering end-to-end fusions with low support (remaining=614)
[2026-06-08T08:45:12] Filtering fusions with no coverage around the breakpoints (remaining=592)
[2026-06-08T08:45:13] Indexing gene sequences 
[2026-06-08T08:45:18] Filtering genes with >=30% identity (remaining=236)
[2026-06-08T08:45:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=159)
[2026-06-08T08:45:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=145)
[2026-06-08T08:45:35] Searching for additional isoforms (remaining=164)
[2026-06-08T08:45:36] Assigning confidence scores to events 
[2026-06-08T08:45:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:39] Writing fusions to file 'aih-tih-sc-00d05f-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:41] Writing discarded fusions to file 'aih-tih-sc-00d05f-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:13] Freeing resources
[2026-06-08T08:46:37] Done (elapsed time=00:11:30, CPU time=00:11:29, peak memory=13gb)