[2026-06-08T08:43:20] Launching Arriba 2.4.0
[2026-06-08T08:43:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:33] Reading chimeric alignments from 'aih-tih-sc-885658-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11075286)
[2026-06-08T08:49:35] Marking multi-mapping alignments (marked=7787359)
[2026-06-08T08:49:40] Detecting strandedness (reverse)
[2026-06-08T08:49:40] Assigning strands to alignments 
[2026-06-08T08:49:42] Annotating alignments 
[2026-06-08T08:50:18] Filtering duplicates (remaining=5470107)
[2026-06-08T08:50:24] 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=4982219)
[2026-06-08T08:50:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4982219)
[2026-06-08T08:50:28] Filtering viral contigs with expression lower than the top 5 (remaining=4982219)
[2026-06-08T08:50:33] Filtering viral contigs with less than 5% coverage (remaining=4982219)
[2026-06-08T08:50:35] Estimating fragment length (mate gap mean=-86.6178, mate gap stddev=28.9816, read length mean=125.062)
[2026-06-08T08:50:35] Filtering read-through fragments with a distance <=10000bp (remaining=4753146)
[2026-06-08T08:50:37] Filtering inconsistently clipped mates (remaining=4639091)
[2026-06-08T08:50:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4464899)
[2026-06-08T08:50:43] Filtering fragments with small insert size (remaining=4463869)
[2026-06-08T08:50:45] Filtering alignments with long gaps (remaining=4463869)
[2026-06-08T08:50:47] Filtering fragments with both mates in the same gene (remaining=4462693)
[2026-06-08T08:50:49] Filtering fusions arising from hairpin structures (remaining=4142325)
[2026-06-08T08:50:52] Filtering reads with a mismatch p-value <=0.01 (remaining=1624597)
[2026-06-08T08:51:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=723096)
[2026-06-08T08:51:12] Finding fusions and counting supporting reads (total=595000)
[2026-06-08T08:51:28] Merging adjacent fusion breakpoints (remaining=589530)
[2026-06-08T08:51:30] Filtering multi-mapping fusions by alignment score and read support (remaining=341855)
[2026-06-08T08:52:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:52:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=339896)
[2026-06-08T08:52:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=206004)
[2026-06-08T08:52:11] Filtering fusions with <2 supporting reads (remaining=20134)
[2026-06-08T08:52:12] Filtering fusions with an e-value >=0.3 (remaining=5102)
[2026-06-08T08:52:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5169)
[2026-06-08T08:52:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5065)
[2026-06-08T08:52:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5065)
[2026-06-08T08:52:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4726)
[2026-06-08T08:52:23] Searching for fusions with spliced split reads (remaining=4802)
[2026-06-08T08:52:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=3369)
[2026-06-08T08:52:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3310)
[2026-06-08T08:52:30] Searching for fusions with >=4 spliced events (remaining=3843)
[2026-06-08T08:52:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1469)
[2026-06-08T08:52:45] Filtering fusions with anchors <=23nt (remaining=1159)
[2026-06-08T08:52:46] Filtering end-to-end fusions with low support (remaining=1114)
[2026-06-08T08:52:47] Filtering fusions with no coverage around the breakpoints (remaining=1082)
[2026-06-08T08:52:47] Indexing gene sequences 
[2026-06-08T08:52:52] Filtering genes with >=30% identity (remaining=394)
[2026-06-08T08:52:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=205)
[2026-06-08T08:52:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=177)
[2026-06-08T08:52:58] Searching for additional isoforms (remaining=223)
[2026-06-08T08:52:59] Assigning confidence scores to events 
[2026-06-08T08:53:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:02] Writing fusions to file 'aih-tih-sc-885658-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:04] Writing discarded fusions to file 'aih-tih-sc-885658-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:30] Freeing resources
[2026-06-08T08:53:47] Done (elapsed time=00:10:27, CPU time=00:10:26, peak memory=15.9gb)