[2026-06-08T07:40:49] Launching Arriba 2.4.0
[2026-06-08T07:40:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:41:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:41:13] Reading chimeric alignments from 'aih-tih-sc-598a93-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=3890264)
[2026-06-08T07:43:44] Marking multi-mapping alignments (marked=2967005)
[2026-06-08T07:43:46] Detecting strandedness (reverse)
[2026-06-08T07:43:46] Assigning strands to alignments 
[2026-06-08T07:43:46] Annotating alignments 
[2026-06-08T07:44:02] Filtering duplicates (remaining=1289562)
[2026-06-08T07:44:05] 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=1075021)
[2026-06-08T07:44:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1075021)
[2026-06-08T07:44:06] Filtering viral contigs with expression lower than the top 5 (remaining=1075021)
[2026-06-08T07:44:08] Filtering viral contigs with less than 5% coverage (remaining=1075021)
[2026-06-08T07:44:09] Estimating fragment length (mate gap mean=-76.6866, mate gap stddev=28.3748, read length mean=110.235)
[2026-06-08T07:44:09] Filtering read-through fragments with a distance <=10000bp (remaining=1036810)
[2026-06-08T07:44:09] Filtering inconsistently clipped mates (remaining=1003092)
[2026-06-08T07:44:10] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=952311)
[2026-06-08T07:44:12] Filtering fragments with small insert size (remaining=951580)
[2026-06-08T07:44:12] Filtering alignments with long gaps (remaining=951580)
[2026-06-08T07:44:13] Filtering fragments with both mates in the same gene (remaining=951127)
[2026-06-08T07:44:14] Filtering fusions arising from hairpin structures (remaining=881175)
[2026-06-08T07:44:15] Filtering reads with a mismatch p-value <=0.01 (remaining=266403)
[2026-06-08T07:44:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=112109)
[2026-06-08T07:44:21] Finding fusions and counting supporting reads (total=106370)
[2026-06-08T07:44:27] Merging adjacent fusion breakpoints (remaining=105610)
[2026-06-08T07:44:27] Filtering multi-mapping fusions by alignment score and read support (remaining=49547)
[2026-06-08T07:44:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:44:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=48990)
[2026-06-08T07:44:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=30324)
[2026-06-08T07:44:43] Filtering fusions with <2 supporting reads (remaining=1680)
[2026-06-08T07:44:43] Filtering fusions with an e-value >=0.3 (remaining=551)
[2026-06-08T07:44:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=576)
[2026-06-08T07:44:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=541)
[2026-06-08T07:44:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=541)
[2026-06-08T07:44:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=532)
[2026-06-08T07:44:47] Searching for fusions with spliced split reads (remaining=565)
[2026-06-08T07:44:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=426)
[2026-06-08T07:44:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=416)
[2026-06-08T07:44:49] Searching for fusions with >=4 spliced events (remaining=434)
[2026-06-08T07:44:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=126)
[2026-06-08T07:45:10] Filtering fusions with anchors <=23nt (remaining=100)
[2026-06-08T07:45:10] Filtering end-to-end fusions with low support (remaining=98)
[2026-06-08T07:45:10] Filtering fusions with no coverage around the breakpoints (remaining=96)
[2026-06-08T07:45:11] Indexing gene sequences 
[2026-06-08T07:45:12] Filtering genes with >=30% identity (remaining=31)
[2026-06-08T07:45:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=16)
[2026-06-08T07:45:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=16)
[2026-06-08T07:45:13] Searching for additional isoforms (remaining=18)
[2026-06-08T07:45:13] Assigning confidence scores to events 
[2026-06-08T07:45:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:45:14] Writing fusions to file 'aih-tih-sc-598a93-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:45:14] Writing discarded fusions to file 'aih-tih-sc-598a93-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:45:24] Freeing resources
[2026-06-08T07:45:33] Done (elapsed time=00:04:44, CPU time=00:04:42, peak memory=8.14gb)