[2026-06-08T08:23:05] Launching Arriba 2.4.0
[2026-06-08T08:23:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:17] Reading chimeric alignments from 'aih-tih-sc-560d56-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=7075175)
[2026-06-08T08:27:08] Marking multi-mapping alignments (marked=4839022)
[2026-06-08T08:27:11] Detecting strandedness (reverse)
[2026-06-08T08:27:11] Assigning strands to alignments 
[2026-06-08T08:27:12] Annotating alignments 
[2026-06-08T08:27:35] Filtering duplicates (remaining=2008273)
[2026-06-08T08:27:38] 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=1828292)
[2026-06-08T08:27:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1828292)
[2026-06-08T08:27:41] Filtering viral contigs with expression lower than the top 5 (remaining=1828292)
[2026-06-08T08:27:44] Filtering viral contigs with less than 5% coverage (remaining=1828292)
[2026-06-08T08:27:45] Estimating fragment length (mate gap mean=-85.1811, mate gap stddev=28.1481, read length mean=123.312)
[2026-06-08T08:27:45] Filtering read-through fragments with a distance <=10000bp (remaining=1754776)
[2026-06-08T08:27:47] Filtering inconsistently clipped mates (remaining=1708881)
[2026-06-08T08:27:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1639593)
[2026-06-08T08:27:50] Filtering fragments with small insert size (remaining=1639069)
[2026-06-08T08:27:51] Filtering alignments with long gaps (remaining=1639069)
[2026-06-08T08:27:52] Filtering fragments with both mates in the same gene (remaining=1638574)
[2026-06-08T08:27:54] Filtering fusions arising from hairpin structures (remaining=1535381)
[2026-06-08T08:27:55] Filtering reads with a mismatch p-value <=0.01 (remaining=609884)
[2026-06-08T08:28:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=202730)
[2026-06-08T08:28:04] Finding fusions and counting supporting reads (total=178251)
[2026-06-08T08:28:12] Merging adjacent fusion breakpoints (remaining=176910)
[2026-06-08T08:28:13] Filtering multi-mapping fusions by alignment score and read support (remaining=96606)
[2026-06-08T08:28:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=95872)
[2026-06-08T08:28:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=55875)
[2026-06-08T08:28:38] Filtering fusions with <2 supporting reads (remaining=4883)
[2026-06-08T08:28:39] Filtering fusions with an e-value >=0.3 (remaining=1298)
[2026-06-08T08:28:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1322)
[2026-06-08T08:28:41] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1272)
[2026-06-08T08:28:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1272)
[2026-06-08T08:28:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1264)
[2026-06-08T08:28:44] Searching for fusions with spliced split reads (remaining=1360)
[2026-06-08T08:28:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=1069)
[2026-06-08T08:28:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1050)
[2026-06-08T08:28:48] Searching for fusions with >=4 spliced events (remaining=1160)
[2026-06-08T08:28:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=371)
[2026-06-08T08:28:59] Filtering fusions with anchors <=23nt (remaining=309)
[2026-06-08T08:28:59] Filtering end-to-end fusions with low support (remaining=301)
[2026-06-08T08:28:59] Filtering fusions with no coverage around the breakpoints (remaining=295)
[2026-06-08T08:29:00] Indexing gene sequences 
[2026-06-08T08:29:02] Filtering genes with >=30% identity (remaining=107)
[2026-06-08T08:29:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=62)
[2026-06-08T08:29:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=59)
[2026-06-08T08:29:04] Searching for additional isoforms (remaining=71)
[2026-06-08T08:29:05] Assigning confidence scores to events 
[2026-06-08T08:29:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:29:06] Writing fusions to file 'aih-tih-sc-560d56-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:29:06] Writing discarded fusions to file 'aih-tih-sc-560d56-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:29:17] Freeing resources
[2026-06-08T08:29:28] Done (elapsed time=00:06:23, CPU time=00:06:22, peak memory=11.3gb)