[2026-06-08T08:31:54] Launching Arriba 2.4.0
[2026-06-08T08:31:54] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:06] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:10] Reading chimeric alignments from 'aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=9281623)
[2026-06-08T08:37:09] Marking multi-mapping alignments (marked=6251518)
[2026-06-08T08:37:13] Detecting strandedness (reverse)
[2026-06-08T08:37:13] Assigning strands to alignments 
[2026-06-08T08:37:15] Annotating alignments 
[2026-06-08T08:37:42] Filtering duplicates (remaining=5009234)
[2026-06-08T08:37:47] 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=4795739)
[2026-06-08T08:37:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4795739)
[2026-06-08T08:37:51] Filtering viral contigs with expression lower than the top 5 (remaining=4795739)
[2026-06-08T08:37:55] Filtering viral contigs with less than 5% coverage (remaining=4795739)
[2026-06-08T08:37:57] Estimating fragment length (mate gap mean=-86.1669, mate gap stddev=27.0665, read length mean=128.013)
[2026-06-08T08:37:57] Filtering read-through fragments with a distance <=10000bp (remaining=4534379)
[2026-06-08T08:37:58] Filtering inconsistently clipped mates (remaining=4446805)
[2026-06-08T08:38:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4306078)
[2026-06-08T08:38:03] Filtering fragments with small insert size (remaining=4305514)
[2026-06-08T08:38:05] Filtering alignments with long gaps (remaining=4305513)
[2026-06-08T08:38:07] Filtering fragments with both mates in the same gene (remaining=4304644)
[2026-06-08T08:38:09] Filtering fusions arising from hairpin structures (remaining=4077719)
[2026-06-08T08:38:10] Filtering reads with a mismatch p-value <=0.01 (remaining=1880293)
[2026-06-08T08:38:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=675217)
[2026-06-08T08:38:28] Finding fusions and counting supporting reads (total=512895)
[2026-06-08T08:38:41] Merging adjacent fusion breakpoints (remaining=507620)
[2026-06-08T08:38:42] Filtering multi-mapping fusions by alignment score and read support (remaining=280169)
[2026-06-08T08:39:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=278917)
[2026-06-08T08:39:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=169477)
[2026-06-08T08:39:15] Filtering fusions with <2 supporting reads (remaining=20275)
[2026-06-08T08:39:15] Filtering fusions with an e-value >=0.3 (remaining=4792)
[2026-06-08T08:39:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4841)
[2026-06-08T08:39:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4773)
[2026-06-08T08:39:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4773)
[2026-06-08T08:39:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4497)
[2026-06-08T08:39:24] Searching for fusions with spliced split reads (remaining=4580)
[2026-06-08T08:39:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=3161)
[2026-06-08T08:39:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3136)
[2026-06-08T08:39:29] Searching for fusions with >=4 spliced events (remaining=3648)
[2026-06-08T08:39:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1408)
[2026-06-08T08:39:46] Filtering fusions with anchors <=23nt (remaining=1209)
[2026-06-08T08:39:46] Filtering end-to-end fusions with low support (remaining=1175)
[2026-06-08T08:39:47] Filtering fusions with no coverage around the breakpoints (remaining=1152)
[2026-06-08T08:39:47] Indexing gene sequences 
[2026-06-08T08:39:52] Filtering genes with >=30% identity (remaining=321)
[2026-06-08T08:39:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=133)
[2026-06-08T08:39:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=116)
[2026-06-08T08:39:57] Searching for additional isoforms (remaining=149)
[2026-06-08T08:39:58] Assigning confidence scores to events 
[2026-06-08T08:40:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:01] Writing fusions to file 'aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:40:02] Writing discarded fusions to file 'aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:40:24] Freeing resources
[2026-06-08T08:40:37] Done (elapsed time=00:08:43, CPU time=00:08:42, peak memory=13.6gb)