[2026-06-08T07:52:39] Launching Arriba 2.4.0
[2026-06-08T07:52:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:52:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:53:05] Reading chimeric alignments from 'aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=5362152)
[2026-06-08T07:57:21] Marking multi-mapping alignments (marked=3676862)
[2026-06-08T07:57:24] Detecting strandedness (reverse)
[2026-06-08T07:57:24] Assigning strands to alignments 
[2026-06-08T07:57:25] Annotating alignments 
[2026-06-08T07:57:49] Filtering duplicates (remaining=1967468)
[2026-06-08T07:57:53] 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=1852055)
[2026-06-08T07:57:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1852055)
[2026-06-08T07:57:56] Filtering viral contigs with expression lower than the top 5 (remaining=1852055)
[2026-06-08T07:57:58] Filtering viral contigs with less than 5% coverage (remaining=1852055)
[2026-06-08T07:58:00] Estimating fragment length (mate gap mean=-81.3074, mate gap stddev=26.9531, read length mean=117.955)
[2026-06-08T07:58:00] Filtering read-through fragments with a distance <=10000bp (remaining=1776784)
[2026-06-08T07:58:01] Filtering inconsistently clipped mates (remaining=1740699)
[2026-06-08T07:58:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1652030)
[2026-06-08T07:58:05] Filtering fragments with small insert size (remaining=1651510)
[2026-06-08T07:58:06] Filtering alignments with long gaps (remaining=1651510)
[2026-06-08T07:58:08] Filtering fragments with both mates in the same gene (remaining=1650930)
[2026-06-08T07:58:09] Filtering fusions arising from hairpin structures (remaining=1582848)
[2026-06-08T07:58:10] Filtering reads with a mismatch p-value <=0.01 (remaining=596268)
[2026-06-08T07:58:17] Filtering reads with low entropy (k-mer content >=60%) (remaining=178287)
[2026-06-08T07:58:21] Finding fusions and counting supporting reads (total=162635)
[2026-06-08T07:58:31] Merging adjacent fusion breakpoints (remaining=161713)
[2026-06-08T07:58:32] Filtering multi-mapping fusions by alignment score and read support (remaining=82352)
[2026-06-08T07:58:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:58:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=81790)
[2026-06-08T07:58:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=53376)
[2026-06-08T07:58:59] Filtering fusions with <2 supporting reads (remaining=4267)
[2026-06-08T07:58:59] Filtering fusions with an e-value >=0.3 (remaining=1114)
[2026-06-08T07:59:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1137)
[2026-06-08T07:59:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1108)
[2026-06-08T07:59:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1108)
[2026-06-08T07:59:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1069)
[2026-06-08T07:59:06] Searching for fusions with spliced split reads (remaining=1151)
[2026-06-08T07:59:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=827)
[2026-06-08T07:59:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=813)
[2026-06-08T07:59:10] Searching for fusions with >=4 spliced events (remaining=898)
[2026-06-08T07:59:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=346)
[2026-06-08T07:59:31] Filtering fusions with anchors <=23nt (remaining=317)
[2026-06-08T07:59:31] Filtering end-to-end fusions with low support (remaining=311)
[2026-06-08T07:59:31] Filtering fusions with no coverage around the breakpoints (remaining=302)
[2026-06-08T07:59:32] Indexing gene sequences 
[2026-06-08T07:59:34] Filtering genes with >=30% identity (remaining=125)
[2026-06-08T07:59:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=78)
[2026-06-08T07:59:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=69)
[2026-06-08T07:59:37] Searching for additional isoforms (remaining=95)
[2026-06-08T07:59:38] Assigning confidence scores to events 
[2026-06-08T07:59:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:59:40] Writing fusions to file 'aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:59:40] Writing discarded fusions to file 'aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:59:54] Freeing resources
[2026-06-08T08:00:05] Done (elapsed time=00:07:26, CPU time=00:07:25, peak memory=9.48gb)