[2026-06-08T08:44:05] Launching Arriba 2.4.0
[2026-06-08T08:44:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:44:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:44:17] Reading chimeric alignments from 'aih-tih-sc-973c73-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10930694)
[2026-06-08T08:50:59] Marking multi-mapping alignments (marked=7007036)
[2026-06-08T08:51:04] Detecting strandedness (reverse)
[2026-06-08T08:51:04] Assigning strands to alignments 
[2026-06-08T08:51:06] Annotating alignments 
[2026-06-08T08:51:41] Filtering duplicates (remaining=6680774)
[2026-06-08T08:51:50] 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=6401910)
[2026-06-08T08:51:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6401910)
[2026-06-08T08:51:55] Filtering viral contigs with expression lower than the top 5 (remaining=6401910)
[2026-06-08T08:52:00] Filtering viral contigs with less than 5% coverage (remaining=6401910)
[2026-06-08T08:52:03] Estimating fragment length (mate gap mean=-85.8953, mate gap stddev=27.818, read length mean=129.045)
[2026-06-08T08:52:03] Filtering read-through fragments with a distance <=10000bp (remaining=6032441)
[2026-06-08T08:52:05] Filtering inconsistently clipped mates (remaining=5938959)
[2026-06-08T08:52:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5792972)
[2026-06-08T08:52:13] Filtering fragments with small insert size (remaining=5792194)
[2026-06-08T08:52:15] Filtering alignments with long gaps (remaining=5792194)
[2026-06-08T08:52:18] Filtering fragments with both mates in the same gene (remaining=5791129)
[2026-06-08T08:52:20] Filtering fusions arising from hairpin structures (remaining=5541406)
[2026-06-08T08:52:23] Filtering reads with a mismatch p-value <=0.01 (remaining=2680440)
[2026-06-08T08:52:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=963927)
[2026-06-08T08:52:48] Finding fusions and counting supporting reads (total=716217)
[2026-06-08T08:53:07] Merging adjacent fusion breakpoints (remaining=709690)
[2026-06-08T08:53:09] Filtering multi-mapping fusions by alignment score and read support (remaining=427671)
[2026-06-08T08:53:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=426106)
[2026-06-08T08:53:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=245264)
[2026-06-08T08:53:55] Filtering fusions with <2 supporting reads (remaining=28465)
[2026-06-08T08:53:56] Filtering fusions with an e-value >=0.3 (remaining=6979)
[2026-06-08T08:53:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7033)
[2026-06-08T08:54:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6941)
[2026-06-08T08:54:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6941)
[2026-06-08T08:54:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6684)
[2026-06-08T08:54:09] Searching for fusions with spliced split reads (remaining=6821)
[2026-06-08T08:54:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=4373)
[2026-06-08T08:54:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4325)
[2026-06-08T08:54:17] Searching for fusions with >=4 spliced events (remaining=5358)
[2026-06-08T08:54:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2533)
[2026-06-08T08:54:35] Filtering fusions with anchors <=23nt (remaining=2183)
[2026-06-08T08:54:35] Filtering end-to-end fusions with low support (remaining=2122)
[2026-06-08T08:54:36] Filtering fusions with no coverage around the breakpoints (remaining=2058)
[2026-06-08T08:54:37] Indexing gene sequences 
[2026-06-08T08:54:46] Filtering genes with >=30% identity (remaining=767)
[2026-06-08T08:54:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=452)
[2026-06-08T08:55:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=325)
[2026-06-08T08:55:04] Searching for additional isoforms (remaining=428)
[2026-06-08T08:55:05] Assigning confidence scores to events 
[2026-06-08T08:55:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:09] Writing fusions to file 'aih-tih-sc-973c73-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:13] Writing discarded fusions to file 'aih-tih-sc-973c73-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:45] Freeing resources
[2026-06-08T08:56:04] Done (elapsed time=00:11:59, CPU time=00:11:59, peak memory=15.3gb)