[2026-06-08T08:52:31] Launching Arriba 2.4.0
[2026-06-08T08:52:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:44] Reading chimeric alignments from 'tih_rna_sample_00673_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11841136)
[2026-06-08T08:59:54] Marking multi-mapping alignments (marked=7219824)
[2026-06-08T09:00:00] Detecting strandedness (reverse)
[2026-06-08T09:00:00] Assigning strands to alignments 
[2026-06-08T09:00:03] Annotating alignments 
[2026-06-08T09:00:49] Filtering duplicates (remaining=5445751)
[2026-06-08T09:00:57] 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=5226531)
[2026-06-08T09:01:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5226531)
[2026-06-08T09:01:02] Filtering viral contigs with expression lower than the top 5 (remaining=5226531)
[2026-06-08T09:01:09] Filtering viral contigs with less than 5% coverage (remaining=5226531)
[2026-06-08T09:01:12] Estimating fragment length (mate gap mean=-91.5573, mate gap stddev=27.7384, read length mean=135.532)
[2026-06-08T09:01:12] Filtering read-through fragments with a distance <=10000bp (remaining=4907281)
[2026-06-08T09:01:15] Filtering inconsistently clipped mates (remaining=4833347)
[2026-06-08T09:01:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4702675)
[2026-06-08T09:01:23] Filtering fragments with small insert size (remaining=4702022)
[2026-06-08T09:01:26] Filtering alignments with long gaps (remaining=4702022)
[2026-06-08T09:01:29] Filtering fragments with both mates in the same gene (remaining=4701369)
[2026-06-08T09:01:31] Filtering fusions arising from hairpin structures (remaining=4466847)
[2026-06-08T09:01:35] Filtering reads with a mismatch p-value <=0.01 (remaining=2021837)
[2026-06-08T09:01:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=745336)
[2026-06-08T09:01:58] Finding fusions and counting supporting reads (total=593567)
[2026-06-08T09:02:17] Merging adjacent fusion breakpoints (remaining=587558)
[2026-06-08T09:02:19] Filtering multi-mapping fusions by alignment score and read support (remaining=369016)
[2026-06-08T09:03:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=367558)
[2026-06-08T09:03:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=194605)
[2026-06-08T09:03:09] Filtering fusions with <2 supporting reads (remaining=25196)
[2026-06-08T09:03:09] Filtering fusions with an e-value >=0.3 (remaining=6186)
[2026-06-08T09:03:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6230)
[2026-06-08T09:03:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6166)
[2026-06-08T09:03:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6166)
[2026-06-08T09:03:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5559)
[2026-06-08T09:03:22] Searching for fusions with spliced split reads (remaining=5619)
[2026-06-08T09:03:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=3866)
[2026-06-08T09:03:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3819)
[2026-06-08T09:03:30] Searching for fusions with >=4 spliced events (remaining=4444)
[2026-06-08T09:03:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1524)
[2026-06-08T09:03:46] Filtering fusions with anchors <=23nt (remaining=1193)
[2026-06-08T09:03:47] Filtering end-to-end fusions with low support (remaining=1129)
[2026-06-08T09:03:47] Filtering fusions with no coverage around the breakpoints (remaining=1092)
[2026-06-08T09:03:48] Indexing gene sequences 
[2026-06-08T09:03:53] Filtering genes with >=30% identity (remaining=319)
[2026-06-08T09:03:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=138)
[2026-06-08T09:03:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=138)
[2026-06-08T09:03:58] Searching for additional isoforms (remaining=160)
[2026-06-08T09:04:00] Assigning confidence scores to events 
[2026-06-08T09:04:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:03] Writing fusions to file 'tih_rna_sample_00673_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:04:05] Writing discarded fusions to file 'tih_rna_sample_00673_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:33] Freeing resources
[2026-06-08T09:04:53] Done (elapsed time=00:12:22, CPU time=00:12:21, peak memory=16.4gb)