[2026-06-08T08:30:28] Launching Arriba 2.4.0
[2026-06-08T08:30:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:44] Reading chimeric alignments from '1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=19412579)
[2026-06-08T08:38:38] Marking multi-mapping alignments (marked=13579789)
[2026-06-08T08:38:46] Detecting strandedness (reverse)
[2026-06-08T08:38:46] Assigning strands to alignments 
[2026-06-08T08:38:50] Annotating alignments 
[2026-06-08T08:39:49] Filtering duplicates (remaining=8693452)
[2026-06-08T08:40:00] 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=7805644)
[2026-06-08T08:40:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7805644)
[2026-06-08T08:40:08] Filtering viral contigs with expression lower than the top 5 (remaining=7805644)
[2026-06-08T08:40:17] Filtering viral contigs with less than 5% coverage (remaining=7805644)
[2026-06-08T08:40:22] Estimating fragment length (mate gap mean=-78.4922, mate gap stddev=26.9466, read length mean=116.451)
[2026-06-08T08:40:22] Filtering read-through fragments with a distance <=10000bp (remaining=7444828)
[2026-06-08T08:40:26] Filtering inconsistently clipped mates (remaining=7274052)
[2026-06-08T08:40:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7130901)
[2026-06-08T08:40:37] Filtering fragments with small insert size (remaining=7127870)
[2026-06-08T08:40:42] Filtering alignments with long gaps (remaining=7127869)
[2026-06-08T08:40:46] Filtering fragments with both mates in the same gene (remaining=7126362)
[2026-06-08T08:40:50] Filtering fusions arising from hairpin structures (remaining=6743705)
[2026-06-08T08:40:55] Filtering reads with a mismatch p-value <=0.01 (remaining=2707272)
[2026-06-08T08:41:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=1031884)
[2026-06-08T08:41:28] Finding fusions and counting supporting reads (total=943423)
[2026-06-08T08:41:55] Merging adjacent fusion breakpoints (remaining=932978)
[2026-06-08T08:41:58] Filtering multi-mapping fusions by alignment score and read support (remaining=468413)
[2026-06-08T08:42:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=466957)
[2026-06-08T08:43:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=316825)
[2026-06-08T08:43:03] Filtering fusions with <2 supporting reads (remaining=19159)
[2026-06-08T08:43:04] Filtering fusions with an e-value >=0.3 (remaining=3876)
[2026-06-08T08:43:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3991)
[2026-06-08T08:43:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3891)
[2026-06-08T08:43:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3891)
[2026-06-08T08:43:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3886)
[2026-06-08T08:43:22] Searching for fusions with spliced split reads (remaining=3948)
[2026-06-08T08:43:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=2767)
[2026-06-08T08:43:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2750)
[2026-06-08T08:43:33] Searching for fusions with >=4 spliced events (remaining=3177)
[2026-06-08T08:43:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1554)
[2026-06-08T08:43:56] Filtering fusions with anchors <=23nt (remaining=1084)
[2026-06-08T08:43:57] Filtering end-to-end fusions with low support (remaining=1036)
[2026-06-08T08:43:58] Filtering fusions with no coverage around the breakpoints (remaining=999)
[2026-06-08T08:43:59] Indexing gene sequences 
[2026-06-08T08:44:04] Filtering genes with >=30% identity (remaining=355)
[2026-06-08T08:44:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=113)
[2026-06-08T08:44:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=103)
[2026-06-08T08:44:10] Searching for additional isoforms (remaining=117)
[2026-06-08T08:44:12] Assigning confidence scores to events 
[2026-06-08T08:44:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:44:16] Writing fusions to file '1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:44:18] Writing discarded fusions to file '1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:57] Freeing resources
[2026-06-08T08:45:27] Done (elapsed time=00:14:59, CPU time=00:14:57, peak memory=23.7gb)