[2026-06-08T08:29:31] Launching Arriba 2.4.0
[2026-06-08T08:29:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:29:44] Reading chimeric alignments from '1173_JXL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=15543123)
[2026-06-08T08:37:12] Marking multi-mapping alignments (marked=10439244)
[2026-06-08T08:37:19] Detecting strandedness (reverse)
[2026-06-08T08:37:19] Assigning strands to alignments 
[2026-06-08T08:37:23] Annotating alignments 
[2026-06-08T08:38:18] Filtering duplicates (remaining=12084376)
[2026-06-08T08:38:32] 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=10404188)
[2026-06-08T08:38:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=10404188)
[2026-06-08T08:38:42] Filtering viral contigs with expression lower than the top 5 (remaining=10404188)
[2026-06-08T08:38:50] Filtering viral contigs with less than 5% coverage (remaining=10404188)
[2026-06-08T08:38:54] Estimating fragment length (mate gap mean=-83.8883, mate gap stddev=27.7949, read length mean=130.675)
[2026-06-08T08:38:55] Filtering read-through fragments with a distance <=10000bp (remaining=10132993)
[2026-06-08T08:38:59] Filtering inconsistently clipped mates (remaining=10042194)
[2026-06-08T08:39:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9837302)
[2026-06-08T08:39:11] Filtering fragments with small insert size (remaining=9836555)
[2026-06-08T08:39:15] Filtering alignments with long gaps (remaining=9836555)
[2026-06-08T08:39:19] Filtering fragments with both mates in the same gene (remaining=9835275)
[2026-06-08T08:39:22] Filtering fusions arising from hairpin structures (remaining=9624015)
[2026-06-08T08:39:26] Filtering reads with a mismatch p-value <=0.01 (remaining=5102269)
[2026-06-08T08:39:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=2788981)
[2026-06-08T08:40:12] Finding fusions and counting supporting reads (total=2565171)
[2026-06-08T08:40:47] Merging adjacent fusion breakpoints (remaining=2559448)
[2026-06-08T08:40:51] Filtering multi-mapping fusions by alignment score and read support (remaining=1417144)
[2026-06-08T08:41:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1416092)
[2026-06-08T08:42:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1261581)
[2026-06-08T08:42:06] Filtering fusions with <2 supporting reads (remaining=33926)
[2026-06-08T08:42:07] Filtering fusions with an e-value >=0.3 (remaining=4811)
[2026-06-08T08:42:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4848)
[2026-06-08T08:42:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4809)
[2026-06-08T08:42:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4809)
[2026-06-08T08:42:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4523)
[2026-06-08T08:42:32] Searching for fusions with spliced split reads (remaining=4627)
[2026-06-08T08:42:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=3133)
[2026-06-08T08:42:45] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3107)
[2026-06-08T08:42:47] Searching for fusions with >=4 spliced events (remaining=4015)
[2026-06-08T08:42:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1743)
[2026-06-08T08:43:04] Filtering fusions with anchors <=23nt (remaining=1415)
[2026-06-08T08:43:05] Filtering end-to-end fusions with low support (remaining=1401)
[2026-06-08T08:43:07] Filtering fusions with no coverage around the breakpoints (remaining=1385)
[2026-06-08T08:43:08] Indexing gene sequences 
[2026-06-08T08:43:14] Filtering genes with >=30% identity (remaining=464)
[2026-06-08T08:43:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=262)
[2026-06-08T08:43:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=219)
[2026-06-08T08:43:28] Searching for additional isoforms (remaining=273)
[2026-06-08T08:43:31] Assigning confidence scores to events 
[2026-06-08T08:43:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:38] Writing fusions to file '1173_JXL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:43:41] Writing discarded fusions to file '1173_JXL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:43] Freeing resources
[2026-06-08T08:45:09] Done (elapsed time=00:15:38, CPU time=00:15:36, peak memory=20.9gb)