[2026-06-08T08:44:28] Launching Arriba 2.4.0
[2026-06-08T08:44:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:44:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:44:43] Reading chimeric alignments from '1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=12129177)
[2026-06-08T08:51:17] Marking multi-mapping alignments (marked=8011908)
[2026-06-08T08:51:21] Detecting strandedness (reverse)
[2026-06-08T08:51:21] Assigning strands to alignments 
[2026-06-08T08:51:24] Annotating alignments 
[2026-06-08T08:51:58] Filtering duplicates (remaining=9718672)
[2026-06-08T08:52:07] 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=8595926)
[2026-06-08T08:52:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8595926)
[2026-06-08T08:52:11] Filtering viral contigs with expression lower than the top 5 (remaining=8595926)
[2026-06-08T08:52:16] Filtering viral contigs with less than 5% coverage (remaining=8595926)
[2026-06-08T08:52:18] Estimating fragment length (mate gap mean=-82.9984, mate gap stddev=28.5205, read length mean=128.11)
[2026-06-08T08:52:18] Filtering read-through fragments with a distance <=10000bp (remaining=8343591)
[2026-06-08T08:52:20] Filtering inconsistently clipped mates (remaining=8276411)
[2026-06-08T08:52:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8116837)
[2026-06-08T08:52:28] Filtering fragments with small insert size (remaining=8116169)
[2026-06-08T08:52:30] Filtering alignments with long gaps (remaining=8116169)
[2026-06-08T08:52:32] Filtering fragments with both mates in the same gene (remaining=8114717)
[2026-06-08T08:52:34] Filtering fusions arising from hairpin structures (remaining=7942196)
[2026-06-08T08:52:36] Filtering reads with a mismatch p-value <=0.01 (remaining=4151769)
[2026-06-08T08:52:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=2125112)
[2026-06-08T08:53:08] Finding fusions and counting supporting reads (total=1958802)
[2026-06-08T08:53:28] Merging adjacent fusion breakpoints (remaining=1953506)
[2026-06-08T08:53:30] Filtering multi-mapping fusions by alignment score and read support (remaining=1136397)
[2026-06-08T08:54:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1135396)
[2026-06-08T08:54:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1025947)
[2026-06-08T08:54:16] Filtering fusions with <2 supporting reads (remaining=27911)
[2026-06-08T08:54:17] Filtering fusions with an e-value >=0.3 (remaining=4259)
[2026-06-08T08:54:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4299)
[2026-06-08T08:54:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4263)
[2026-06-08T08:54:23] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4263)
[2026-06-08T08:54:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4170)
[2026-06-08T08:54:32] Searching for fusions with spliced split reads (remaining=4300)
[2026-06-08T08:54:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=3030)
[2026-06-08T08:54:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2999)
[2026-06-08T08:54:42] Searching for fusions with >=4 spliced events (remaining=3711)
[2026-06-08T08:54:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1658)
[2026-06-08T08:54:57] Filtering fusions with anchors <=23nt (remaining=1281)
[2026-06-08T08:54:58] Filtering end-to-end fusions with low support (remaining=1253)
[2026-06-08T08:54:59] Filtering fusions with no coverage around the breakpoints (remaining=1228)
[2026-06-08T08:55:00] Indexing gene sequences 
[2026-06-08T08:55:06] Filtering genes with >=30% identity (remaining=550)
[2026-06-08T08:55:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=391)
[2026-06-08T08:55:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=268)
[2026-06-08T08:55:18] Searching for additional isoforms (remaining=379)
[2026-06-08T08:55:20] Assigning confidence scores to events 
[2026-06-08T08:55:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:27] Writing fusions to file '1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:30] Writing discarded fusions to file '1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:12] Freeing resources
[2026-06-08T08:56:31] Done (elapsed time=00:12:03, CPU time=00:12:02, peak memory=17.2gb)