[2026-06-03T20:17:53] Launching Arriba 2.4.0
[2026-06-03T20:17:53] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:18:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:18:05] Reading chimeric alignments from 'aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11227407)
[2026-06-03T20:24:57] Marking multi-mapping alignments (marked=7592659)
[2026-06-03T20:25:02] Detecting strandedness (reverse)
[2026-06-03T20:25:02] Assigning strands to alignments 
[2026-06-03T20:25:04] Annotating alignments 
[2026-06-03T20:25:46] Filtering duplicates (remaining=6201597)
[2026-06-03T20:25:54] 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=5722436)
[2026-06-03T20:25:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5722436)
[2026-06-03T20:25:59] Filtering viral contigs with expression lower than the top 5 (remaining=5722436)
[2026-06-03T20:26:04] Filtering viral contigs with less than 5% coverage (remaining=5722436)
[2026-06-03T20:26:07] Estimating fragment length (mate gap mean=-87.146, mate gap stddev=28.2612, read length mean=126.753)
[2026-06-03T20:26:07] Filtering read-through fragments with a distance <=10000bp (remaining=5407580)
[2026-06-03T20:26:09] Filtering inconsistently clipped mates (remaining=5282691)
[2026-06-03T20:26:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5121844)
[2026-06-03T20:26:17] Filtering fragments with small insert size (remaining=5120595)
[2026-06-03T20:26:19] Filtering alignments with long gaps (remaining=5120595)
[2026-06-03T20:26:22] Filtering fragments with both mates in the same gene (remaining=5119509)
[2026-06-03T20:26:24] Filtering fusions arising from hairpin structures (remaining=4773156)
[2026-06-03T20:26:27] Filtering reads with a mismatch p-value <=0.01 (remaining=1896083)
[2026-06-03T20:26:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=878583)
[2026-06-03T20:26:52] Finding fusions and counting supporting reads (total=713091)
[2026-06-03T20:27:11] Merging adjacent fusion breakpoints (remaining=704587)
[2026-06-03T20:27:13] Filtering multi-mapping fusions by alignment score and read support (remaining=417794)
[2026-06-03T20:27:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:28:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=415936)
[2026-06-03T20:28:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=241211)
[2026-06-03T20:28:01] Filtering fusions with <2 supporting reads (remaining=26556)
[2026-06-03T20:28:02] Filtering fusions with an e-value >=0.3 (remaining=6869)
[2026-06-03T20:28:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6915)
[2026-06-03T20:28:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6809)
[2026-06-03T20:28:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6809)
[2026-06-03T20:28:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5540)
[2026-06-03T20:28:15] Searching for fusions with spliced split reads (remaining=5653)
[2026-06-03T20:28:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=3731)
[2026-06-03T20:28:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3682)
[2026-06-03T20:28:23] Searching for fusions with >=4 spliced events (remaining=4480)
[2026-06-03T20:28:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1883)
[2026-06-03T20:28:40] Filtering fusions with anchors <=23nt (remaining=1533)
[2026-06-03T20:28:41] Filtering end-to-end fusions with low support (remaining=1482)
[2026-06-03T20:28:42] Filtering fusions with no coverage around the breakpoints (remaining=1454)
[2026-06-03T20:28:43] Indexing gene sequences 
[2026-06-03T20:28:49] Filtering genes with >=30% identity (remaining=426)
[2026-06-03T20:28:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=188)
[2026-06-03T20:28:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=173)
[2026-06-03T20:28:56] Searching for additional isoforms (remaining=211)
[2026-06-03T20:28:57] Assigning confidence scores to events 
[2026-06-03T20:29:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:29:01] Writing fusions to file 'aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:29:03] Writing discarded fusions to file 'aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:29:35] Freeing resources
[2026-06-03T20:29:54] Done (elapsed time=00:12:01, CPU time=00:12:00, peak memory=16.1gb)