[2026-06-08T08:37:51] Launching Arriba 2.4.0
[2026-06-08T08:37:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:03] Reading chimeric alignments from 'aih-tih-sc-5c902f-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12943597)
[2026-06-08T08:43:14] Marking multi-mapping alignments (marked=9349156)
[2026-06-08T08:43:19] Detecting strandedness (reverse)
[2026-06-08T08:43:19] Assigning strands to alignments 
[2026-06-08T08:43:21] Annotating alignments 
[2026-06-08T08:43:59] Filtering duplicates (remaining=4019730)
[2026-06-08T08:44:05] 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=3674323)
[2026-06-08T08:44:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3674323)
[2026-06-08T08:44:09] Filtering viral contigs with expression lower than the top 5 (remaining=3674323)
[2026-06-08T08:44:14] Filtering viral contigs with less than 5% coverage (remaining=3674323)
[2026-06-08T08:44:17] Estimating fragment length (mate gap mean=-82.412, mate gap stddev=27.8376, read length mean=122.08)
[2026-06-08T08:44:17] Filtering read-through fragments with a distance <=10000bp (remaining=3535309)
[2026-06-08T08:44:19] Filtering inconsistently clipped mates (remaining=3461171)
[2026-06-08T08:44:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3291495)
[2026-06-08T08:44:25] Filtering fragments with small insert size (remaining=3290571)
[2026-06-08T08:44:27] Filtering alignments with long gaps (remaining=3290571)
[2026-06-08T08:44:30] Filtering fragments with both mates in the same gene (remaining=3289803)
[2026-06-08T08:44:32] Filtering fusions arising from hairpin structures (remaining=3118078)
[2026-06-08T08:44:34] Filtering reads with a mismatch p-value <=0.01 (remaining=1192024)
[2026-06-08T08:44:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=344055)
[2026-06-08T08:44:50] Finding fusions and counting supporting reads (total=292388)
[2026-06-08T08:45:05] Merging adjacent fusion breakpoints (remaining=289586)
[2026-06-08T08:45:06] Filtering multi-mapping fusions by alignment score and read support (remaining=146201)
[2026-06-08T08:45:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=145193)
[2026-06-08T08:45:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=87394)
[2026-06-08T08:45:49] Filtering fusions with <2 supporting reads (remaining=7221)
[2026-06-08T08:45:50] Filtering fusions with an e-value >=0.3 (remaining=1770)
[2026-06-08T08:45:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1817)
[2026-06-08T08:45:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1733)
[2026-06-08T08:45:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1733)
[2026-06-08T08:45:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1708)
[2026-06-08T08:46:00] Searching for fusions with spliced split reads (remaining=1798)
[2026-06-08T08:46:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=1349)
[2026-06-08T08:46:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1336)
[2026-06-08T08:46:06] Searching for fusions with >=4 spliced events (remaining=1437)
[2026-06-08T08:46:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=492)
[2026-06-08T08:46:19] Filtering fusions with anchors <=23nt (remaining=391)
[2026-06-08T08:46:20] Filtering end-to-end fusions with low support (remaining=385)
[2026-06-08T08:46:20] Filtering fusions with no coverage around the breakpoints (remaining=378)
[2026-06-08T08:46:21] Indexing gene sequences 
[2026-06-08T08:46:23] Filtering genes with >=30% identity (remaining=145)
[2026-06-08T08:46:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=69)
[2026-06-08T08:46:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=63)
[2026-06-08T08:46:27] Searching for additional isoforms (remaining=71)
[2026-06-08T08:46:28] Assigning confidence scores to events 
[2026-06-08T08:46:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:30] Writing fusions to file 'aih-tih-sc-5c902f-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:46:30] Writing discarded fusions to file 'aih-tih-sc-5c902f-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:49] Freeing resources
[2026-06-08T08:47:07] Done (elapsed time=00:09:16, CPU time=00:09:14, peak memory=17.1gb)