[2026-06-08T07:50:36] Launching Arriba 2.4.0
[2026-06-08T07:50:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:50:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:51:02] Reading chimeric alignments from 'aih-tih-sc-97c26d-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=4519873)
[2026-06-08T07:54:49] Marking multi-mapping alignments (marked=3081873)
[2026-06-08T07:54:51] Detecting strandedness (reverse)
[2026-06-08T07:54:51] Assigning strands to alignments 
[2026-06-08T07:54:52] Annotating alignments 
[2026-06-08T07:55:10] Filtering duplicates (remaining=2036942)
[2026-06-08T07:55:14] 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=1945374)
[2026-06-08T07:55:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1945374)
[2026-06-08T07:55:16] Filtering viral contigs with expression lower than the top 5 (remaining=1945374)
[2026-06-08T07:55:18] Filtering viral contigs with less than 5% coverage (remaining=1945374)
[2026-06-08T07:55:19] Estimating fragment length (mate gap mean=-79.5909, mate gap stddev=26.6319, read length mean=115.314)
[2026-06-08T07:55:19] Filtering read-through fragments with a distance <=10000bp (remaining=1852151)
[2026-06-08T07:55:20] Filtering inconsistently clipped mates (remaining=1823356)
[2026-06-08T07:55:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1748656)
[2026-06-08T07:55:22] Filtering fragments with small insert size (remaining=1748184)
[2026-06-08T07:55:23] Filtering alignments with long gaps (remaining=1748184)
[2026-06-08T07:55:24] Filtering fragments with both mates in the same gene (remaining=1747442)
[2026-06-08T07:55:25] Filtering fusions arising from hairpin structures (remaining=1699724)
[2026-06-08T07:55:26] Filtering reads with a mismatch p-value <=0.01 (remaining=682667)
[2026-06-08T07:55:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=221397)
[2026-06-08T07:55:35] Finding fusions and counting supporting reads (total=189765)
[2026-06-08T07:55:43] Merging adjacent fusion breakpoints (remaining=188328)
[2026-06-08T07:55:43] Filtering multi-mapping fusions by alignment score and read support (remaining=97047)
[2026-06-08T07:56:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:56:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=96552)
[2026-06-08T07:56:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=67809)
[2026-06-08T07:56:04] Filtering fusions with <2 supporting reads (remaining=7327)
[2026-06-08T07:56:04] Filtering fusions with an e-value >=0.3 (remaining=1858)
[2026-06-08T07:56:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1876)
[2026-06-08T07:56:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1842)
[2026-06-08T07:56:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1842)
[2026-06-08T07:56:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1834)
[2026-06-08T07:56:10] Searching for fusions with spliced split reads (remaining=1936)
[2026-06-08T07:56:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=1450)
[2026-06-08T07:56:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1439)
[2026-06-08T07:56:13] Searching for fusions with >=4 spliced events (remaining=1614)
[2026-06-08T07:56:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=612)
[2026-06-08T07:56:35] Filtering fusions with anchors <=23nt (remaining=534)
[2026-06-08T07:56:35] Filtering end-to-end fusions with low support (remaining=527)
[2026-06-08T07:56:35] Filtering fusions with no coverage around the breakpoints (remaining=513)
[2026-06-08T07:56:36] Indexing gene sequences 
[2026-06-08T07:56:40] Filtering genes with >=30% identity (remaining=203)
[2026-06-08T07:56:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=115)
[2026-06-08T07:56:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=94)
[2026-06-08T07:56:42] Searching for additional isoforms (remaining=112)
[2026-06-08T07:56:43] Assigning confidence scores to events 
[2026-06-08T07:56:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:56:44] Writing fusions to file 'aih-tih-sc-97c26d-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:56:45] Writing discarded fusions to file 'aih-tih-sc-97c26d-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:56:59] Freeing resources
[2026-06-08T07:57:08] Done (elapsed time=00:06:32, CPU time=00:06:31, peak memory=8.67gb)