[2026-06-08T08:39:22] Launching Arriba 2.4.0
[2026-06-08T08:39:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:41] Reading chimeric alignments from 'aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=13963659)
[2026-06-08T08:47:45] Marking multi-mapping alignments (marked=9985877)
[2026-06-08T08:47:50] Detecting strandedness (reverse)
[2026-06-08T08:47:50] Assigning strands to alignments 
[2026-06-08T08:47:53] Annotating alignments 
[2026-06-08T08:48:37] Filtering duplicates (remaining=6230591)
[2026-06-08T08:48:46] 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=5574482)
[2026-06-08T08:48:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5574482)
[2026-06-08T08:48:51] Filtering viral contigs with expression lower than the top 5 (remaining=5574482)
[2026-06-08T08:48:56] Filtering viral contigs with less than 5% coverage (remaining=5574482)
[2026-06-08T08:48:59] Estimating fragment length (mate gap mean=-81.71, mate gap stddev=28.3709, read length mean=115.375)
[2026-06-08T08:48:59] Filtering read-through fragments with a distance <=10000bp (remaining=5294597)
[2026-06-08T08:49:01] Filtering inconsistently clipped mates (remaining=5172528)
[2026-06-08T08:49:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4991822)
[2026-06-08T08:49:09] Filtering fragments with small insert size (remaining=4989987)
[2026-06-08T08:49:11] Filtering alignments with long gaps (remaining=4989987)
[2026-06-08T08:49:14] Filtering fragments with both mates in the same gene (remaining=4988824)
[2026-06-08T08:49:17] Filtering fusions arising from hairpin structures (remaining=4686372)
[2026-06-08T08:49:20] Filtering reads with a mismatch p-value <=0.01 (remaining=1552212)
[2026-06-08T08:49:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=719660)
[2026-06-08T08:49:42] Finding fusions and counting supporting reads (total=601837)
[2026-06-08T08:50:02] Merging adjacent fusion breakpoints (remaining=595095)
[2026-06-08T08:50:03] Filtering multi-mapping fusions by alignment score and read support (remaining=338904)
[2026-06-08T08:50:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=337424)
[2026-06-08T08:50:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=205484)
[2026-06-08T08:50:53] Filtering fusions with <2 supporting reads (remaining=19787)
[2026-06-08T08:50:54] Filtering fusions with an e-value >=0.3 (remaining=4656)
[2026-06-08T08:50:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4706)
[2026-06-08T08:50:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4614)
[2026-06-08T08:51:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4614)
[2026-06-08T08:51:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4523)
[2026-06-08T08:51:07] Searching for fusions with spliced split reads (remaining=4591)
[2026-06-08T08:51:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=3278)
[2026-06-08T08:51:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3242)
[2026-06-08T08:51:14] Searching for fusions with >=4 spliced events (remaining=3690)
[2026-06-08T08:51:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1546)
[2026-06-08T08:51:38] Filtering fusions with anchors <=23nt (remaining=1092)
[2026-06-08T08:51:38] Filtering end-to-end fusions with low support (remaining=1034)
[2026-06-08T08:51:39] Filtering fusions with no coverage around the breakpoints (remaining=1004)
[2026-06-08T08:51:40] Indexing gene sequences 
[2026-06-08T08:51:45] Filtering genes with >=30% identity (remaining=377)
[2026-06-08T08:51:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=170)
[2026-06-08T08:51:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=161)
[2026-06-08T08:51:51] Searching for additional isoforms (remaining=180)
[2026-06-08T08:51:52] Assigning confidence scores to events 
[2026-06-08T08:51:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:56] Writing fusions to file 'aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:58] Writing discarded fusions to file 'aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:30] Freeing resources
[2026-06-08T08:52:52] Done (elapsed time=00:13:30, CPU time=00:13:30, peak memory=18.8gb)