[2026-06-08T07:58:14] Launching Arriba 2.4.0
[2026-06-08T07:58:14] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:58:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:58:34] Reading chimeric alignments from '1173_IT6_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=8464549)
[2026-06-08T08:04:14] Marking multi-mapping alignments (marked=6102110)
[2026-06-08T08:04:18] Detecting strandedness (reverse)
[2026-06-08T08:04:18] Assigning strands to alignments 
[2026-06-08T08:04:19] Annotating alignments 
[2026-06-08T08:04:49] Filtering duplicates (remaining=5453565)
[2026-06-08T08:04:57] 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=4795999)
[2026-06-08T08:04:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4795999)
[2026-06-08T08:05:00] Filtering viral contigs with expression lower than the top 5 (remaining=4795999)
[2026-06-08T08:05:04] Filtering viral contigs with less than 5% coverage (remaining=4795999)
[2026-06-08T08:05:05] Estimating fragment length (mate gap mean=-78.0027, mate gap stddev=27.7868, read length mean=115.374)
[2026-06-08T08:05:06] Filtering read-through fragments with a distance <=10000bp (remaining=4653635)
[2026-06-08T08:05:07] Filtering inconsistently clipped mates (remaining=4553130)
[2026-06-08T08:05:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4470440)
[2026-06-08T08:05:12] Filtering fragments with small insert size (remaining=4469528)
[2026-06-08T08:05:14] Filtering alignments with long gaps (remaining=4469528)
[2026-06-08T08:05:15] Filtering fragments with both mates in the same gene (remaining=4468666)
[2026-06-08T08:05:17] Filtering fusions arising from hairpin structures (remaining=4223748)
[2026-06-08T08:05:19] Filtering reads with a mismatch p-value <=0.01 (remaining=1915108)
[2026-06-08T08:05:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=740376)
[2026-06-08T08:05:38] Finding fusions and counting supporting reads (total=666549)
[2026-06-08T08:05:54] Merging adjacent fusion breakpoints (remaining=662655)
[2026-06-08T08:05:56] Filtering multi-mapping fusions by alignment score and read support (remaining=349305)
[2026-06-08T08:06:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:06:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=348539)
[2026-06-08T08:06:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=262997)
[2026-06-08T08:06:35] Filtering fusions with <2 supporting reads (remaining=11122)
[2026-06-08T08:06:35] Filtering fusions with an e-value >=0.3 (remaining=2452)
[2026-06-08T08:06:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2540)
[2026-06-08T08:06:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2499)
[2026-06-08T08:06:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2499)
[2026-06-08T08:06:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2486)
[2026-06-08T08:06:45] Searching for fusions with spliced split reads (remaining=2622)
[2026-06-08T08:06:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=1970)
[2026-06-08T08:06:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1949)
[2026-06-08T08:06:52] Searching for fusions with >=4 spliced events (remaining=2145)
[2026-06-08T08:06:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=819)
[2026-06-08T08:07:11] Filtering fusions with anchors <=23nt (remaining=666)
[2026-06-08T08:07:12] Filtering end-to-end fusions with low support (remaining=642)
[2026-06-08T08:07:12] Filtering fusions with no coverage around the breakpoints (remaining=635)
[2026-06-08T08:07:13] Indexing gene sequences 
[2026-06-08T08:07:18] Filtering genes with >=30% identity (remaining=198)
[2026-06-08T08:07:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=88)
[2026-06-08T08:07:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=79)
[2026-06-08T08:07:23] Searching for additional isoforms (remaining=94)
[2026-06-08T08:07:24] Assigning confidence scores to events 
[2026-06-08T08:07:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:07:27] Writing fusions to file '1173_IT6_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:07:28] Writing discarded fusions to file '1173_IT6_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:08:03] Freeing resources
[2026-06-08T08:08:22] Done (elapsed time=00:10:08, CPU time=00:10:06, peak memory=12.8gb)