[2026-06-08T08:56:20] Launching Arriba 2.4.0
[2026-06-08T08:56:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:56:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:56:32] Reading chimeric alignments from 'aih-tih-sc-9be8d4-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10219975)
[2026-06-08T09:03:54] Marking multi-mapping alignments (marked=6241002)
[2026-06-08T09:03:59] Detecting strandedness (reverse)
[2026-06-08T09:03:59] Assigning strands to alignments 
[2026-06-08T09:04:01] Annotating alignments 
[2026-06-08T09:04:40] Filtering duplicates (remaining=6327881)
[2026-06-08T09:04:48] 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=6006210)
[2026-06-08T09:04:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6006210)
[2026-06-08T09:04:53] Filtering viral contigs with expression lower than the top 5 (remaining=6006210)
[2026-06-08T09:04:58] Filtering viral contigs with less than 5% coverage (remaining=6006210)
[2026-06-08T09:05:01] Estimating fragment length (mate gap mean=-86.3656, mate gap stddev=28.7913, read length mean=130.772)
[2026-06-08T09:05:01] Filtering read-through fragments with a distance <=10000bp (remaining=5534105)
[2026-06-08T09:05:03] Filtering inconsistently clipped mates (remaining=5424456)
[2026-06-08T09:05:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5303886)
[2026-06-08T09:05:11] Filtering fragments with small insert size (remaining=5302731)
[2026-06-08T09:05:13] Filtering alignments with long gaps (remaining=5302731)
[2026-06-08T09:05:16] Filtering fragments with both mates in the same gene (remaining=5301622)
[2026-06-08T09:05:18] Filtering fusions arising from hairpin structures (remaining=4939204)
[2026-06-08T09:05:21] Filtering reads with a mismatch p-value <=0.01 (remaining=2356364)
[2026-06-08T09:05:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=1135924)
[2026-06-08T09:05:47] Finding fusions and counting supporting reads (total=832247)
[2026-06-08T09:06:06] Merging adjacent fusion breakpoints (remaining=820780)
[2026-06-08T09:06:08] Filtering multi-mapping fusions by alignment score and read support (remaining=536838)
[2026-06-08T09:06:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:06:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=534006)
[2026-06-08T09:06:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=272422)
[2026-06-08T09:06:52] Filtering fusions with <2 supporting reads (remaining=38997)
[2026-06-08T09:06:53] Filtering fusions with an e-value >=0.3 (remaining=10158)
[2026-06-08T09:06:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10221)
[2026-06-08T09:06:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10091)
[2026-06-08T09:06:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10091)
[2026-06-08T09:07:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8630)
[2026-06-08T09:07:05] Searching for fusions with spliced split reads (remaining=8654)
[2026-06-08T09:07:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=5147)
[2026-06-08T09:07:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5095)
[2026-06-08T09:07:12] Searching for fusions with >=4 spliced events (remaining=6139)
[2026-06-08T09:07:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2182)
[2026-06-08T09:07:29] Filtering fusions with anchors <=23nt (remaining=1818)
[2026-06-08T09:07:30] Filtering end-to-end fusions with low support (remaining=1764)
[2026-06-08T09:07:31] Filtering fusions with no coverage around the breakpoints (remaining=1729)
[2026-06-08T09:07:31] Indexing gene sequences 
[2026-06-08T09:07:37] Filtering genes with >=30% identity (remaining=487)
[2026-06-08T09:07:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=199)
[2026-06-08T09:07:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=191)
[2026-06-08T09:07:47] Searching for additional isoforms (remaining=236)
[2026-06-08T09:07:48] Assigning confidence scores to events 
[2026-06-08T09:07:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:07:52] Writing fusions to file 'aih-tih-sc-9be8d4-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:07:54] Writing discarded fusions to file 'aih-tih-sc-9be8d4-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:08:26] Freeing resources
[2026-06-08T09:08:44] Done (elapsed time=00:12:24, CPU time=00:12:23, peak memory=15gb)