[2026-06-08T09:06:33] Launching Arriba 2.4.0
[2026-06-08T09:06:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:06:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:06:53] Reading chimeric alignments from 'aih-tih-sc-377071-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10493738)
[2026-06-08T09:15:22] Marking multi-mapping alignments (marked=6707265)
[2026-06-08T09:15:26] Detecting strandedness (reverse)
[2026-06-08T09:15:26] Assigning strands to alignments 
[2026-06-08T09:15:28] Annotating alignments 
[2026-06-08T09:16:02] Filtering duplicates (remaining=7243881)
[2026-06-08T09:16:09] 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=6804167)
[2026-06-08T09:16:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6804167)
[2026-06-08T09:16:13] Filtering viral contigs with expression lower than the top 5 (remaining=6804167)
[2026-06-08T09:16:17] Filtering viral contigs with less than 5% coverage (remaining=6804167)
[2026-06-08T09:16:20] Estimating fragment length (mate gap mean=-82.7675, mate gap stddev=32.4024, read length mean=133.442)
[2026-06-08T09:16:20] Filtering read-through fragments with a distance <=10000bp (remaining=6430738)
[2026-06-08T09:16:22] Filtering inconsistently clipped mates (remaining=6312086)
[2026-06-08T09:16:23] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6137055)
[2026-06-08T09:16:28] Filtering fragments with small insert size (remaining=6136195)
[2026-06-08T09:16:30] Filtering alignments with long gaps (remaining=6136194)
[2026-06-08T09:16:32] Filtering fragments with both mates in the same gene (remaining=6134987)
[2026-06-08T09:16:34] Filtering fusions arising from hairpin structures (remaining=5729325)
[2026-06-08T09:16:36] Filtering reads with a mismatch p-value <=0.01 (remaining=2744460)
[2026-06-08T09:16:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=1399754)
[2026-06-08T09:17:06] Finding fusions and counting supporting reads (total=1212611)
[2026-06-08T09:17:23] Merging adjacent fusion breakpoints (remaining=1206763)
[2026-06-08T09:17:25] Filtering multi-mapping fusions by alignment score and read support (remaining=802612)
[2026-06-08T09:17:56] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:18:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=799847)
[2026-06-08T09:18:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=592563)
[2026-06-08T09:18:06] Filtering fusions with <2 supporting reads (remaining=40896)
[2026-06-08T09:18:07] Filtering fusions with an e-value >=0.3 (remaining=11646)
[2026-06-08T09:18:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11708)
[2026-06-08T09:18:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11605)
[2026-06-08T09:18:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11605)
[2026-06-08T09:18:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7439)
[2026-06-08T09:18:19] Searching for fusions with spliced split reads (remaining=7477)
[2026-06-08T09:18:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=3914)
[2026-06-08T09:18:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3857)
[2026-06-08T09:18:27] Searching for fusions with >=4 spliced events (remaining=4678)
[2026-06-08T09:18:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1909)
[2026-06-08T09:18:49] Filtering fusions with anchors <=23nt (remaining=1463)
[2026-06-08T09:18:50] Filtering end-to-end fusions with low support (remaining=1425)
[2026-06-08T09:18:51] Filtering fusions with no coverage around the breakpoints (remaining=1390)
[2026-06-08T09:18:52] Indexing gene sequences 
[2026-06-08T09:18:58] Filtering genes with >=30% identity (remaining=432)
[2026-06-08T09:19:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=226)
[2026-06-08T09:19:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=212)
[2026-06-08T09:19:11] Searching for additional isoforms (remaining=277)
[2026-06-08T09:19:13] Assigning confidence scores to events 
[2026-06-08T09:19:17] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:19:17] Writing fusions to file 'aih-tih-sc-377071-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:19:21] Writing discarded fusions to file 'aih-tih-sc-377071-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:19:56] Freeing resources
[2026-06-08T09:20:13] Done (elapsed time=00:13:40, CPU time=00:13:39, peak memory=15.4gb)