[2026-06-08T07:45:32] Launching Arriba 2.4.0
[2026-06-08T07:45:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:45:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:45:57] Reading chimeric alignments from 'aih-tih-sc-976eb1-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=3911394)
[2026-06-08T07:48:42] Marking multi-mapping alignments (marked=2790042)
[2026-06-08T07:48:44] Detecting strandedness (reverse)
[2026-06-08T07:48:44] Assigning strands to alignments 
[2026-06-08T07:48:44] Annotating alignments 
[2026-06-08T07:49:00] Filtering duplicates (remaining=1356198)
[2026-06-08T07:49:02] 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=1263998)
[2026-06-08T07:49:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1263998)
[2026-06-08T07:49:04] Filtering viral contigs with expression lower than the top 5 (remaining=1263998)
[2026-06-08T07:49:05] Filtering viral contigs with less than 5% coverage (remaining=1263998)
[2026-06-08T07:49:06] Estimating fragment length (mate gap mean=-79.5775, mate gap stddev=28.7472, read length mean=118.693)
[2026-06-08T07:49:07] Filtering read-through fragments with a distance <=10000bp (remaining=1226278)
[2026-06-08T07:49:07] Filtering inconsistently clipped mates (remaining=1194935)
[2026-06-08T07:49:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1133233)
[2026-06-08T07:49:09] Filtering fragments with small insert size (remaining=1132843)
[2026-06-08T07:49:10] Filtering alignments with long gaps (remaining=1132843)
[2026-06-08T07:49:11] Filtering fragments with both mates in the same gene (remaining=1132336)
[2026-06-08T07:49:12] Filtering fusions arising from hairpin structures (remaining=1072272)
[2026-06-08T07:49:13] Filtering reads with a mismatch p-value <=0.01 (remaining=401508)
[2026-06-08T07:49:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=110479)
[2026-06-08T07:49:19] Finding fusions and counting supporting reads (total=102642)
[2026-06-08T07:49:25] Merging adjacent fusion breakpoints (remaining=102120)
[2026-06-08T07:49:25] Filtering multi-mapping fusions by alignment score and read support (remaining=49007)
[2026-06-08T07:49:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:49:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=48643)
[2026-06-08T07:49:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=31283)
[2026-06-08T07:49:43] Filtering fusions with <2 supporting reads (remaining=2013)
[2026-06-08T07:49:43] Filtering fusions with an e-value >=0.3 (remaining=674)
[2026-06-08T07:49:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=699)
[2026-06-08T07:49:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=667)
[2026-06-08T07:49:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=667)
[2026-06-08T07:49:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=662)
[2026-06-08T07:49:47] Searching for fusions with spliced split reads (remaining=691)
[2026-06-08T07:49:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=541)
[2026-06-08T07:49:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=532)
[2026-06-08T07:49:49] Searching for fusions with >=4 spliced events (remaining=555)
[2026-06-08T07:49:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=188)
[2026-06-08T07:50:10] Filtering fusions with anchors <=23nt (remaining=165)
[2026-06-08T07:50:10] Filtering end-to-end fusions with low support (remaining=162)
[2026-06-08T07:50:10] Filtering fusions with no coverage around the breakpoints (remaining=156)
[2026-06-08T07:50:10] Indexing gene sequences 
[2026-06-08T07:50:12] Filtering genes with >=30% identity (remaining=76)
[2026-06-08T07:50:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=58)
[2026-06-08T07:50:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=58)
[2026-06-08T07:50:13] Searching for additional isoforms (remaining=62)
[2026-06-08T07:50:13] Assigning confidence scores to events 
[2026-06-08T07:50:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:50:15] Writing fusions to file 'aih-tih-sc-976eb1-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:50:15] Writing discarded fusions to file 'aih-tih-sc-976eb1-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:50:25] Freeing resources
[2026-06-08T07:50:33] Done (elapsed time=00:05:01, CPU time=00:05:01, peak memory=8.02gb)