[2026-06-08T08:01:47] Launching Arriba 2.4.0
[2026-06-08T08:01:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:02:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:02:08] Reading chimeric alignments from 'aih-tih-sc-284856-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=2405099)
[2026-06-08T08:04:11] Marking multi-mapping alignments (marked=1466280)
[2026-06-08T08:04:12] Detecting strandedness (reverse)
[2026-06-08T08:04:12] Assigning strands to alignments 
[2026-06-08T08:04:13] Annotating alignments 
[2026-06-08T08:04:21] Filtering duplicates (remaining=1889775)
[2026-06-08T08:04:22] 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=1816133)
[2026-06-08T08:04:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1816133)
[2026-06-08T08:04:23] Filtering viral contigs with expression lower than the top 5 (remaining=1816133)
[2026-06-08T08:04:24] Filtering viral contigs with less than 5% coverage (remaining=1816133)
[2026-06-08T08:04:25] Estimating fragment length (mate gap mean=-87.1591, mate gap stddev=28.656, read length mean=133.138)
[2026-06-08T08:04:25] Filtering read-through fragments with a distance <=10000bp (remaining=1671159)
[2026-06-08T08:04:25] Filtering inconsistently clipped mates (remaining=1641928)
[2026-06-08T08:04:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1611024)
[2026-06-08T08:04:27] Filtering fragments with small insert size (remaining=1610820)
[2026-06-08T08:04:27] Filtering alignments with long gaps (remaining=1610820)
[2026-06-08T08:04:28] Filtering fragments with both mates in the same gene (remaining=1610492)
[2026-06-08T08:04:28] Filtering fusions arising from hairpin structures (remaining=1511788)
[2026-06-08T08:04:29] Filtering reads with a mismatch p-value <=0.01 (remaining=772821)
[2026-06-08T08:04:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=375155)
[2026-06-08T08:04:36] Finding fusions and counting supporting reads (total=304299)
[2026-06-08T08:04:40] Merging adjacent fusion breakpoints (remaining=302379)
[2026-06-08T08:04:41] Filtering multi-mapping fusions by alignment score and read support (remaining=194472)
[2026-06-08T08:04:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:04:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=193707)
[2026-06-08T08:04:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=102968)
[2026-06-08T08:04:51] Filtering fusions with <2 supporting reads (remaining=14333)
[2026-06-08T08:04:51] Filtering fusions with an e-value >=0.3 (remaining=4353)
[2026-06-08T08:04:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4394)
[2026-06-08T08:04:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4380)
[2026-06-08T08:04:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4380)
[2026-06-08T08:04:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3696)
[2026-06-08T08:04:54] Searching for fusions with spliced split reads (remaining=3750)
[2026-06-08T08:04:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=2539)
[2026-06-08T08:04:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2510)
[2026-06-08T08:04:56] Searching for fusions with >=4 spliced events (remaining=2803)
[2026-06-08T08:04:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=825)
[2026-06-08T08:05:14] Filtering fusions with anchors <=23nt (remaining=706)
[2026-06-08T08:05:14] Filtering end-to-end fusions with low support (remaining=695)
[2026-06-08T08:05:14] Filtering fusions with no coverage around the breakpoints (remaining=674)
[2026-06-08T08:05:14] Indexing gene sequences 
[2026-06-08T08:05:19] Filtering genes with >=30% identity (remaining=284)
[2026-06-08T08:05:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=222)
[2026-06-08T08:05:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=196)
[2026-06-08T08:05:24] Searching for additional isoforms (remaining=250)
[2026-06-08T08:05:25] Assigning confidence scores to events 
[2026-06-08T08:05:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:05:26] Writing fusions to file 'aih-tih-sc-284856-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:05:28] Writing discarded fusions to file 'aih-tih-sc-284856-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:05:38] Freeing resources
[2026-06-08T08:05:44] Done (elapsed time=00:03:57, CPU time=00:03:56, peak memory=6.73gb)