[2026-06-08T07:49:35] Launching Arriba 2.4.0
[2026-06-08T07:49:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:49:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:49:58] Reading chimeric alignments from 'aih-tih-sc-62dadb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=4328725)
[2026-06-08T07:53:20] Marking multi-mapping alignments (marked=2978764)
[2026-06-08T07:53:22] Detecting strandedness (reverse)
[2026-06-08T07:53:22] Assigning strands to alignments 
[2026-06-08T07:53:22] Annotating alignments 
[2026-06-08T07:53:39] Filtering duplicates (remaining=2232672)
[2026-06-08T07:53:43] 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=2092219)
[2026-06-08T07:53:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2092219)
[2026-06-08T07:53:45] Filtering viral contigs with expression lower than the top 5 (remaining=2092219)
[2026-06-08T07:53:46] Filtering viral contigs with less than 5% coverage (remaining=2092219)
[2026-06-08T07:53:48] Estimating fragment length (mate gap mean=-83.6586, mate gap stddev=27.6149, read length mean=122.788)
[2026-06-08T07:53:48] Filtering read-through fragments with a distance <=10000bp (remaining=2000736)
[2026-06-08T07:53:49] Filtering inconsistently clipped mates (remaining=1958956)
[2026-06-08T07:53:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1889625)
[2026-06-08T07:53:51] Filtering fragments with small insert size (remaining=1889297)
[2026-06-08T07:53:52] Filtering alignments with long gaps (remaining=1889297)
[2026-06-08T07:53:53] Filtering fragments with both mates in the same gene (remaining=1888791)
[2026-06-08T07:53:54] Filtering fusions arising from hairpin structures (remaining=1781972)
[2026-06-08T07:53:55] Filtering reads with a mismatch p-value <=0.01 (remaining=777159)
[2026-06-08T07:54:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=242362)
[2026-06-08T07:54:05] Finding fusions and counting supporting reads (total=208913)
[2026-06-08T07:54:13] Merging adjacent fusion breakpoints (remaining=206854)
[2026-06-08T07:54:13] Filtering multi-mapping fusions by alignment score and read support (remaining=111625)
[2026-06-08T07:54:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:54:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=110937)
[2026-06-08T07:54:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=64914)
[2026-06-08T07:54:34] Filtering fusions with <2 supporting reads (remaining=6254)
[2026-06-08T07:54:34] Filtering fusions with an e-value >=0.3 (remaining=1755)
[2026-06-08T07:54:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1807)
[2026-06-08T07:54:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1766)
[2026-06-08T07:54:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1766)
[2026-06-08T07:54:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1708)
[2026-06-08T07:54:39] Searching for fusions with spliced split reads (remaining=1842)
[2026-06-08T07:54:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=1363)
[2026-06-08T07:54:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1351)
[2026-06-08T07:54:42] Searching for fusions with >=4 spliced events (remaining=1473)
[2026-06-08T07:54:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=485)
[2026-06-08T07:55:04] Filtering fusions with anchors <=23nt (remaining=404)
[2026-06-08T07:55:05] Filtering end-to-end fusions with low support (remaining=391)
[2026-06-08T07:55:05] Filtering fusions with no coverage around the breakpoints (remaining=382)
[2026-06-08T07:55:05] Indexing gene sequences 
[2026-06-08T07:55:08] Filtering genes with >=30% identity (remaining=130)
[2026-06-08T07:55:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=86)
[2026-06-08T07:55:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=83)
[2026-06-08T07:55:10] Searching for additional isoforms (remaining=96)
[2026-06-08T07:55:11] Assigning confidence scores to events 
[2026-06-08T07:55:13] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:55:13] Writing fusions to file 'aih-tih-sc-62dadb-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:55:13] Writing discarded fusions to file 'aih-tih-sc-62dadb-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:55:29] Freeing resources
[2026-06-08T07:55:38] Done (elapsed time=00:06:03, CPU time=00:06:02, peak memory=8.53gb)