[2026-06-03T20:27:39] Launching Arriba 2.4.0
[2026-06-03T20:27:39] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:27:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:27:50] Reading chimeric alignments from 'aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10742091)
[2026-06-03T20:34:22] Marking multi-mapping alignments (marked=6894113)
[2026-06-03T20:34:26] Detecting strandedness (reverse)
[2026-06-03T20:34:26] Assigning strands to alignments 
[2026-06-03T20:34:28] Annotating alignments 
[2026-06-03T20:35:03] Filtering duplicates (remaining=6489264)
[2026-06-03T20:35:11] 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=6205774)
[2026-06-03T20:35:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6205774)
[2026-06-03T20:35:16] Filtering viral contigs with expression lower than the top 5 (remaining=6205774)
[2026-06-03T20:35:21] Filtering viral contigs with less than 5% coverage (remaining=6205774)
[2026-06-03T20:35:23] Estimating fragment length (mate gap mean=-83.5087, mate gap stddev=27.3529, read length mean=120.509)
[2026-06-03T20:35:24] Filtering read-through fragments with a distance <=10000bp (remaining=5706454)
[2026-06-03T20:35:26] Filtering inconsistently clipped mates (remaining=5573052)
[2026-06-03T20:35:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5424995)
[2026-06-03T20:35:32] Filtering fragments with small insert size (remaining=5423363)
[2026-06-03T20:35:35] Filtering alignments with long gaps (remaining=5423363)
[2026-06-03T20:35:37] Filtering fragments with both mates in the same gene (remaining=5422211)
[2026-06-03T20:35:39] Filtering fusions arising from hairpin structures (remaining=5048882)
[2026-06-03T20:35:42] Filtering reads with a mismatch p-value <=0.01 (remaining=2004714)
[2026-06-03T20:35:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=1080831)
[2026-06-03T20:36:04] Finding fusions and counting supporting reads (total=849236)
[2026-06-03T20:36:22] Merging adjacent fusion breakpoints (remaining=837958)
[2026-06-03T20:36:24] Filtering multi-mapping fusions by alignment score and read support (remaining=527967)
[2026-06-03T20:36:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:37:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=526906)
[2026-06-03T20:37:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=292535)
[2026-06-03T20:37:06] Filtering fusions with <2 supporting reads (remaining=30574)
[2026-06-03T20:37:07] Filtering fusions with an e-value >=0.3 (remaining=6175)
[2026-06-03T20:37:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6260)
[2026-06-03T20:37:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6168)
[2026-06-03T20:37:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6168)
[2026-06-03T20:37:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6074)
[2026-06-03T20:37:21] Searching for fusions with spliced split reads (remaining=6192)
[2026-06-03T20:37:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=4152)
[2026-06-03T20:37:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4111)
[2026-06-03T20:37:28] Searching for fusions with >=4 spliced events (remaining=5010)
[2026-06-03T20:37:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2118)
[2026-06-03T20:37:46] Filtering fusions with anchors <=23nt (remaining=1730)
[2026-06-03T20:37:47] Filtering end-to-end fusions with low support (remaining=1685)
[2026-06-03T20:37:47] Filtering fusions with no coverage around the breakpoints (remaining=1666)
[2026-06-03T20:37:48] Indexing gene sequences 
[2026-06-03T20:37:54] Filtering genes with >=30% identity (remaining=561)
[2026-06-03T20:37:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=233)
[2026-06-03T20:38:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=196)
[2026-06-03T20:38:04] Searching for additional isoforms (remaining=251)
[2026-06-03T20:38:06] Assigning confidence scores to events 
[2026-06-03T20:38:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:38:10] Writing fusions to file 'aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:38:12] Writing discarded fusions to file 'aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:38:40] Freeing resources
[2026-06-03T20:38:57] Done (elapsed time=00:11:18, CPU time=00:11:18, peak memory=15.6gb)