[2026-06-03T19:39:29] Launching Arriba 2.4.0
[2026-06-03T19:39:29] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:39:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:39:44] Reading chimeric alignments from 'aih-tih-sc-607ec3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9067235)
[2026-06-03T19:46:05] Marking multi-mapping alignments (marked=6787696)
[2026-06-03T19:46:10] Detecting strandedness (reverse)
[2026-06-03T19:46:10] Assigning strands to alignments 
[2026-06-03T19:46:12] Annotating alignments 
[2026-06-03T19:46:53] Filtering duplicates (remaining=3943270)
[2026-06-03T19:47:02] 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=3495170)
[2026-06-03T19:47:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3495170)
[2026-06-03T19:47:07] Filtering viral contigs with expression lower than the top 5 (remaining=3495170)
[2026-06-03T19:47:13] Filtering viral contigs with less than 5% coverage (remaining=3495170)
[2026-06-03T19:47:16] Estimating fragment length (mate gap mean=-80.8835, mate gap stddev=27.6403, read length mean=117.309)
[2026-06-03T19:47:16] Filtering read-through fragments with a distance <=10000bp (remaining=3305332)
[2026-06-03T19:47:19] Filtering inconsistently clipped mates (remaining=3218316)
[2026-06-03T19:47:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3100660)
[2026-06-03T19:47:26] Filtering fragments with small insert size (remaining=3099440)
[2026-06-03T19:47:29] Filtering alignments with long gaps (remaining=3099440)
[2026-06-03T19:47:32] Filtering fragments with both mates in the same gene (remaining=3098742)
[2026-06-03T19:47:35] Filtering fusions arising from hairpin structures (remaining=2880477)
[2026-06-03T19:47:38] Filtering reads with a mismatch p-value <=0.01 (remaining=1062281)
[2026-06-03T19:47:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=442627)
[2026-06-03T19:47:57] Finding fusions and counting supporting reads (total=365697)
[2026-06-03T19:48:22] Merging adjacent fusion breakpoints (remaining=362115)
[2026-06-03T19:48:24] Filtering multi-mapping fusions by alignment score and read support (remaining=195002)
[2026-06-03T19:49:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:49:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=193978)
[2026-06-03T19:49:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=112426)
[2026-06-03T19:49:25] Filtering fusions with <2 supporting reads (remaining=10270)
[2026-06-03T19:49:25] Filtering fusions with an e-value >=0.3 (remaining=2597)
[2026-06-03T19:49:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2648)
[2026-06-03T19:49:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2609)
[2026-06-03T19:49:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2609)
[2026-06-03T19:49:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2555)
[2026-06-03T19:49:38] Searching for fusions with spliced split reads (remaining=2687)
[2026-06-03T19:49:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=1962)
[2026-06-03T19:49:45] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1945)
[2026-06-03T19:49:45] Searching for fusions with >=4 spliced events (remaining=2163)
[2026-06-03T19:49:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=781)
[2026-06-03T19:50:07] Filtering fusions with anchors <=23nt (remaining=630)
[2026-06-03T19:50:08] Filtering end-to-end fusions with low support (remaining=612)
[2026-06-03T19:50:08] Filtering fusions with no coverage around the breakpoints (remaining=596)
[2026-06-03T19:50:09] Indexing gene sequences 
[2026-06-03T19:50:13] Filtering genes with >=30% identity (remaining=199)
[2026-06-03T19:50:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=84)
[2026-06-03T19:50:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=84)
[2026-06-03T19:50:17] Searching for additional isoforms (remaining=98)
[2026-06-03T19:50:18] Assigning confidence scores to events 
[2026-06-03T19:50:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:50:21] Writing fusions to file 'aih-tih-sc-607ec3-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:50:22] Writing discarded fusions to file 'aih-tih-sc-607ec3-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:50:52] Freeing resources
[2026-06-03T19:51:10] Done (elapsed time=00:11:41, CPU time=00:11:40, peak memory=13.5gb)