[2026-06-08T08:27:02] Launching Arriba 2.4.0
[2026-06-08T08:27:02] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:15] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:19] Reading chimeric alignments from 'aih-tih-sc-027d27-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11144828)
[2026-06-08T08:34:01] Marking multi-mapping alignments (marked=7469590)
[2026-06-08T08:34:05] Detecting strandedness (reverse)
[2026-06-08T08:34:05] Assigning strands to alignments 
[2026-06-08T08:34:07] Annotating alignments 
[2026-06-08T08:34:41] Filtering duplicates (remaining=6238279)
[2026-06-08T08:34:48] 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=5928848)
[2026-06-08T08:34:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5928848)
[2026-06-08T08:34:52] Filtering viral contigs with expression lower than the top 5 (remaining=5928848)
[2026-06-08T08:34:57] Filtering viral contigs with less than 5% coverage (remaining=5928848)
[2026-06-08T08:34:59] Estimating fragment length (mate gap mean=-86.0051, mate gap stddev=27.8187, read length mean=127.997)
[2026-06-08T08:34:59] Filtering read-through fragments with a distance <=10000bp (remaining=5632889)
[2026-06-08T08:35:01] Filtering inconsistently clipped mates (remaining=5541825)
[2026-06-08T08:35:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5324894)
[2026-06-08T08:35:07] Filtering fragments with small insert size (remaining=5324089)
[2026-06-08T08:35:09] Filtering alignments with long gaps (remaining=5324089)
[2026-06-08T08:35:12] Filtering fragments with both mates in the same gene (remaining=5323096)
[2026-06-08T08:35:14] Filtering fusions arising from hairpin structures (remaining=5064266)
[2026-06-08T08:35:17] Filtering reads with a mismatch p-value <=0.01 (remaining=2386768)
[2026-06-08T08:35:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=806643)
[2026-06-08T08:35:40] Finding fusions and counting supporting reads (total=606740)
[2026-06-08T08:35:55] Merging adjacent fusion breakpoints (remaining=601033)
[2026-06-08T08:35:57] Filtering multi-mapping fusions by alignment score and read support (remaining=342895)
[2026-06-08T08:36:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=341154)
[2026-06-08T08:36:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=205971)
[2026-06-08T08:36:36] Filtering fusions with <2 supporting reads (remaining=25471)
[2026-06-08T08:36:37] Filtering fusions with an e-value >=0.3 (remaining=6911)
[2026-06-08T08:36:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6964)
[2026-06-08T08:36:41] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6868)
[2026-06-08T08:36:42] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6868)
[2026-06-08T08:36:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6574)
[2026-06-08T08:36:48] Searching for fusions with spliced split reads (remaining=6694)
[2026-06-08T08:36:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=4561)
[2026-06-08T08:36:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4484)
[2026-06-08T08:36:55] Searching for fusions with >=4 spliced events (remaining=5063)
[2026-06-08T08:36:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1864)
[2026-06-08T08:37:16] Filtering fusions with anchors <=23nt (remaining=1525)
[2026-06-08T08:37:16] Filtering end-to-end fusions with low support (remaining=1478)
[2026-06-08T08:37:17] Filtering fusions with no coverage around the breakpoints (remaining=1441)
[2026-06-08T08:37:17] Indexing gene sequences 
[2026-06-08T08:37:23] Filtering genes with >=30% identity (remaining=461)
[2026-06-08T08:37:25] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=233)
[2026-06-08T08:37:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=221)
[2026-06-08T08:37:29] Searching for additional isoforms (remaining=285)
[2026-06-08T08:37:30] Assigning confidence scores to events 
[2026-06-08T08:37:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:34] Writing fusions to file 'aih-tih-sc-027d27-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:37:35] Writing discarded fusions to file 'aih-tih-sc-027d27-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:06] Freeing resources
[2026-06-08T08:38:24] Done (elapsed time=00:11:22, CPU time=00:11:22, peak memory=15.5gb)