[2026-06-08T09:43:14] Launching Arriba 2.4.0
[2026-06-08T09:43:14] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:43:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:43:27] Reading chimeric alignments from 'aih-tih-sc-9ee8d4-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8525084)
[2026-06-08T09:49:17] Marking multi-mapping alignments (marked=5440076)
[2026-06-08T09:49:20] Detecting strandedness (reverse)
[2026-06-08T09:49:20] Assigning strands to alignments 
[2026-06-08T09:49:22] Annotating alignments 
[2026-06-08T09:49:48] Filtering duplicates (remaining=5400107)
[2026-06-08T09:49:53] 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=5145767)
[2026-06-08T09:49:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5145767)
[2026-06-08T09:49:56] Filtering viral contigs with expression lower than the top 5 (remaining=5145767)
[2026-06-08T09:50:00] Filtering viral contigs with less than 5% coverage (remaining=5145767)
[2026-06-08T09:50:02] Estimating fragment length (mate gap mean=-85.9369, mate gap stddev=28.5585, read length mean=130.475)
[2026-06-08T09:50:02] Filtering read-through fragments with a distance <=10000bp (remaining=4808028)
[2026-06-08T09:50:04] Filtering inconsistently clipped mates (remaining=4713384)
[2026-06-08T09:50:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4580668)
[2026-06-08T09:50:09] Filtering fragments with small insert size (remaining=4579910)
[2026-06-08T09:50:11] Filtering alignments with long gaps (remaining=4579908)
[2026-06-08T09:50:12] Filtering fragments with both mates in the same gene (remaining=4579027)
[2026-06-08T09:50:14] Filtering fusions arising from hairpin structures (remaining=4266384)
[2026-06-08T09:50:16] Filtering reads with a mismatch p-value <=0.01 (remaining=2028129)
[2026-06-08T09:50:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=845026)
[2026-06-08T09:50:35] Finding fusions and counting supporting reads (total=672097)
[2026-06-08T09:50:48] Merging adjacent fusion breakpoints (remaining=664839)
[2026-06-08T09:50:49] Filtering multi-mapping fusions by alignment score and read support (remaining=419011)
[2026-06-08T09:51:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:51:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=417212)
[2026-06-08T09:51:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=225568)
[2026-06-08T09:51:21] Filtering fusions with <2 supporting reads (remaining=27600)
[2026-06-08T09:51:21] Filtering fusions with an e-value >=0.3 (remaining=7563)
[2026-06-08T09:51:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7611)
[2026-06-08T09:51:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7548)
[2026-06-08T09:51:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7548)
[2026-06-08T09:51:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6283)
[2026-06-08T09:51:32] Searching for fusions with spliced split reads (remaining=6411)
[2026-06-08T09:51:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=4082)
[2026-06-08T09:51:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4033)
[2026-06-08T09:51:38] Searching for fusions with >=4 spliced events (remaining=4787)
[2026-06-08T09:51:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1957)
[2026-06-08T09:51:55] Filtering fusions with anchors <=23nt (remaining=1601)
[2026-06-08T09:51:55] Filtering end-to-end fusions with low support (remaining=1554)
[2026-06-08T09:51:56] Filtering fusions with no coverage around the breakpoints (remaining=1513)
[2026-06-08T09:51:57] Indexing gene sequences 
[2026-06-08T09:52:02] Filtering genes with >=30% identity (remaining=484)
[2026-06-08T09:52:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=220)
[2026-06-08T09:52:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=196)
[2026-06-08T09:52:10] Searching for additional isoforms (remaining=243)
[2026-06-08T09:52:11] Assigning confidence scores to events 
[2026-06-08T09:52:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:52:14] Writing fusions to file 'aih-tih-sc-9ee8d4-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:52:16] Writing discarded fusions to file 'aih-tih-sc-9ee8d4-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:52:40] Freeing resources
[2026-06-08T09:52:55] Done (elapsed time=00:09:41, CPU time=00:09:39, peak memory=13.2gb)