[2026-06-08T08:28:09] Launching Arriba 2.4.0
[2026-06-08T08:28:09] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:22] Reading chimeric alignments from 'tih_rna_sample_00124_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=7267730)
[2026-06-08T08:33:20] Marking multi-mapping alignments (marked=4347826)
[2026-06-08T08:33:23] Detecting strandedness (reverse)
[2026-06-08T08:33:23] Assigning strands to alignments 
[2026-06-08T08:33:24] Annotating alignments 
[2026-06-08T08:33:48] Filtering duplicates (remaining=4123972)
[2026-06-08T08:33:52] 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=3976908)
[2026-06-08T08:33:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3976908)
[2026-06-08T08:33:55] Filtering viral contigs with expression lower than the top 5 (remaining=3976908)
[2026-06-08T08:33:58] Filtering viral contigs with less than 5% coverage (remaining=3976908)
[2026-06-08T08:34:00] Estimating fragment length (mate gap mean=-88.3694, mate gap stddev=29.1708, read length mean=134.532)
[2026-06-08T08:34:00] Filtering read-through fragments with a distance <=10000bp (remaining=3677055)
[2026-06-08T08:34:01] Filtering inconsistently clipped mates (remaining=3612744)
[2026-06-08T08:34:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3514523)
[2026-06-08T08:34:05] Filtering fragments with small insert size (remaining=3513906)
[2026-06-08T08:34:07] Filtering alignments with long gaps (remaining=3513904)
[2026-06-08T08:34:08] Filtering fragments with both mates in the same gene (remaining=3513214)
[2026-06-08T08:34:10] Filtering fusions arising from hairpin structures (remaining=3302511)
[2026-06-08T08:34:11] Filtering reads with a mismatch p-value <=0.01 (remaining=1479365)
[2026-06-08T08:34:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=742190)
[2026-06-08T08:34:26] Finding fusions and counting supporting reads (total=552566)
[2026-06-08T08:34:37] Merging adjacent fusion breakpoints (remaining=547272)
[2026-06-08T08:34:38] Filtering multi-mapping fusions by alignment score and read support (remaining=357188)
[2026-06-08T08:35:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=355418)
[2026-06-08T08:35:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=179271)
[2026-06-08T08:35:06] Filtering fusions with <2 supporting reads (remaining=28939)
[2026-06-08T08:35:07] Filtering fusions with an e-value >=0.3 (remaining=8725)
[2026-06-08T08:35:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8777)
[2026-06-08T08:35:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8702)
[2026-06-08T08:35:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8702)
[2026-06-08T08:35:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6857)
[2026-06-08T08:35:14] Searching for fusions with spliced split reads (remaining=6970)
[2026-06-08T08:35:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=4480)
[2026-06-08T08:35:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4386)
[2026-06-08T08:35:19] Searching for fusions with >=4 spliced events (remaining=4913)
[2026-06-08T08:35:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1516)
[2026-06-08T08:35:35] Filtering fusions with anchors <=23nt (remaining=1148)
[2026-06-08T08:35:35] Filtering end-to-end fusions with low support (remaining=1119)
[2026-06-08T08:35:36] Filtering fusions with no coverage around the breakpoints (remaining=1088)
[2026-06-08T08:35:36] Indexing gene sequences 
[2026-06-08T08:35:41] Filtering genes with >=30% identity (remaining=364)
[2026-06-08T08:35:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=202)
[2026-06-08T08:35:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-08T08:35:46] Searching for additional isoforms (remaining=234)
[2026-06-08T08:35:47] Assigning confidence scores to events 
[2026-06-08T08:35:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:50] Writing fusions to file 'tih_rna_sample_00124_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:35:51] Writing discarded fusions to file 'tih_rna_sample_00124_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:10] Freeing resources
[2026-06-08T08:36:22] Done (elapsed time=00:08:13, CPU time=00:08:12, peak memory=11.8gb)