[2026-06-08T08:36:24] Launching Arriba 2.4.0
[2026-06-08T08:36:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:44] Reading chimeric alignments from '1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=15720152)
[2026-06-08T08:44:53] Marking multi-mapping alignments (marked=10875979)
[2026-06-08T08:45:01] Detecting strandedness (reverse)
[2026-06-08T08:45:01] Assigning strands to alignments 
[2026-06-08T08:45:05] Annotating alignments 
[2026-06-08T08:46:13] Filtering duplicates (remaining=6788604)
[2026-06-08T08:46:25] 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=6303974)
[2026-06-08T08:46:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6303974)
[2026-06-08T08:46:32] Filtering viral contigs with expression lower than the top 5 (remaining=6303974)
[2026-06-08T08:46:39] Filtering viral contigs with less than 5% coverage (remaining=6303974)
[2026-06-08T08:46:43] Estimating fragment length (mate gap mean=-80.7882, mate gap stddev=27.6151, read length mean=119.19)
[2026-06-08T08:46:43] Filtering read-through fragments with a distance <=10000bp (remaining=6114832)
[2026-06-08T08:46:47] Filtering inconsistently clipped mates (remaining=5982705)
[2026-06-08T08:46:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5846032)
[2026-06-08T08:46:56] Filtering fragments with small insert size (remaining=5844199)
[2026-06-08T08:46:59] Filtering alignments with long gaps (remaining=5844199)
[2026-06-08T08:47:03] Filtering fragments with both mates in the same gene (remaining=5843046)
[2026-06-08T08:47:07] Filtering fusions arising from hairpin structures (remaining=5519304)
[2026-06-08T08:47:11] Filtering reads with a mismatch p-value <=0.01 (remaining=2353750)
[2026-06-08T08:47:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=802982)
[2026-06-08T08:47:41] Finding fusions and counting supporting reads (total=693959)
[2026-06-08T08:48:08] Merging adjacent fusion breakpoints (remaining=687804)
[2026-06-08T08:48:10] Filtering multi-mapping fusions by alignment score and read support (remaining=375730)
[2026-06-08T08:49:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=374692)
[2026-06-08T08:49:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=266377)
[2026-06-08T08:49:38] Filtering fusions with <2 supporting reads (remaining=16366)
[2026-06-08T08:49:39] Filtering fusions with an e-value >=0.3 (remaining=3384)
[2026-06-08T08:49:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3466)
[2026-06-08T08:49:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3406)
[2026-06-08T08:49:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3407)
[2026-06-08T08:49:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3390)
[2026-06-08T08:50:00] Searching for fusions with spliced split reads (remaining=3443)
[2026-06-08T08:50:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=2572)
[2026-06-08T08:50:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2535)
[2026-06-08T08:50:12] Searching for fusions with >=4 spliced events (remaining=2827)
[2026-06-08T08:50:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1013)
[2026-06-08T08:50:33] Filtering fusions with anchors <=23nt (remaining=882)
[2026-06-08T08:50:34] Filtering end-to-end fusions with low support (remaining=819)
[2026-06-08T08:50:35] Filtering fusions with no coverage around the breakpoints (remaining=783)
[2026-06-08T08:50:36] Indexing gene sequences 
[2026-06-08T08:50:43] Filtering genes with >=30% identity (remaining=297)
[2026-06-08T08:50:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=172)
[2026-06-08T08:50:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=150)
[2026-06-08T08:50:50] Searching for additional isoforms (remaining=186)
[2026-06-08T08:50:52] Assigning confidence scores to events 
[2026-06-08T08:50:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:57] Writing fusions to file '1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:50:59] Writing discarded fusions to file '1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:49] Freeing resources
[2026-06-08T08:52:19] Done (elapsed time=00:15:55, CPU time=00:15:54, peak memory=19.9gb)