[2026-06-08T08:26:08] Launching Arriba 2.4.0
[2026-06-08T08:26:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:26:20] Reading chimeric alignments from 'tih_rna_sample_00124_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=7569204)
[2026-06-08T08:31:26] Marking multi-mapping alignments (marked=4621480)
[2026-06-08T08:31:29] Detecting strandedness (reverse)
[2026-06-08T08:31:29] Assigning strands to alignments 
[2026-06-08T08:31:30] Annotating alignments 
[2026-06-08T08:31:57] Filtering duplicates (remaining=3511648)
[2026-06-08T08:32:01] 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=3370612)
[2026-06-08T08:32:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3370612)
[2026-06-08T08:32:03] Filtering viral contigs with expression lower than the top 5 (remaining=3370612)
[2026-06-08T08:32:07] Filtering viral contigs with less than 5% coverage (remaining=3370612)
[2026-06-08T08:32:08] Estimating fragment length (mate gap mean=-86.6477, mate gap stddev=29.7801, read length mean=131.445)
[2026-06-08T08:32:08] Filtering read-through fragments with a distance <=10000bp (remaining=3147576)
[2026-06-08T08:32:10] Filtering inconsistently clipped mates (remaining=3098312)
[2026-06-08T08:32:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3006624)
[2026-06-08T08:32:14] Filtering fragments with small insert size (remaining=3005994)
[2026-06-08T08:32:15] Filtering alignments with long gaps (remaining=3005994)
[2026-06-08T08:32:17] Filtering fragments with both mates in the same gene (remaining=3005388)
[2026-06-08T08:32:18] Filtering fusions arising from hairpin structures (remaining=2861259)
[2026-06-08T08:32:20] Filtering reads with a mismatch p-value <=0.01 (remaining=1208311)
[2026-06-08T08:32:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=545355)
[2026-06-08T08:32:34] Finding fusions and counting supporting reads (total=437507)
[2026-06-08T08:32:45] Merging adjacent fusion breakpoints (remaining=432712)
[2026-06-08T08:32:46] Filtering multi-mapping fusions by alignment score and read support (remaining=277687)
[2026-06-08T08:33:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:13] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=276159)
[2026-06-08T08:33:13] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=140777)
[2026-06-08T08:33:14] Filtering fusions with <2 supporting reads (remaining=20442)
[2026-06-08T08:33:14] Filtering fusions with an e-value >=0.3 (remaining=6348)
[2026-06-08T08:33:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6388)
[2026-06-08T08:33:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6307)
[2026-06-08T08:33:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6307)
[2026-06-08T08:33:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4884)
[2026-06-08T08:33:21] Searching for fusions with spliced split reads (remaining=4994)
[2026-06-08T08:33:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=3372)
[2026-06-08T08:33:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3293)
[2026-06-08T08:33:26] Searching for fusions with >=4 spliced events (remaining=3637)
[2026-06-08T08:33:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1087)
[2026-06-08T08:33:41] Filtering fusions with anchors <=23nt (remaining=805)
[2026-06-08T08:33:41] Filtering end-to-end fusions with low support (remaining=774)
[2026-06-08T08:33:41] Filtering fusions with no coverage around the breakpoints (remaining=756)
[2026-06-08T08:33:42] Indexing gene sequences 
[2026-06-08T08:33:45] Filtering genes with >=30% identity (remaining=270)
[2026-06-08T08:33:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=162)
[2026-06-08T08:33:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=160)
[2026-06-08T08:33:49] Searching for additional isoforms (remaining=185)
[2026-06-08T08:33:50] Assigning confidence scores to events 
[2026-06-08T08:33:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:33:52] Writing fusions to file 'tih_rna_sample_00124_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:33:53] Writing discarded fusions to file 'tih_rna_sample_00124_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:10] Freeing resources
[2026-06-08T08:34:22] Done (elapsed time=00:08:14, CPU time=00:08:13, peak memory=12gb)