[2026-06-08T08:25:28] Launching Arriba 2.4.0
[2026-06-08T08:25:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:46] Reading chimeric alignments from 'tih_rna_sample_00637_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10705193)
[2026-06-08T08:32:49] Marking multi-mapping alignments (marked=7010502)
[2026-06-08T08:32:53] Detecting strandedness (reverse)
[2026-06-08T08:32:53] Assigning strands to alignments 
[2026-06-08T08:32:55] Annotating alignments 
[2026-06-08T08:33:28] Filtering duplicates (remaining=6055877)
[2026-06-08T08:33:35] 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=5710275)
[2026-06-08T08:33:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5710275)
[2026-06-08T08:33:39] Filtering viral contigs with expression lower than the top 5 (remaining=5710275)
[2026-06-08T08:33:43] Filtering viral contigs with less than 5% coverage (remaining=5710275)
[2026-06-08T08:33:46] Estimating fragment length (mate gap mean=-86.5862, mate gap stddev=28.633, read length mean=127.845)
[2026-06-08T08:33:46] Filtering read-through fragments with a distance <=10000bp (remaining=5449798)
[2026-06-08T08:33:48] Filtering inconsistently clipped mates (remaining=5332008)
[2026-06-08T08:33:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5202253)
[2026-06-08T08:33:53] Filtering fragments with small insert size (remaining=5201441)
[2026-06-08T08:33:55] Filtering alignments with long gaps (remaining=5201441)
[2026-06-08T08:33:57] Filtering fragments with both mates in the same gene (remaining=5200400)
[2026-06-08T08:33:59] Filtering fusions arising from hairpin structures (remaining=4826879)
[2026-06-08T08:34:01] Filtering reads with a mismatch p-value <=0.01 (remaining=2345393)
[2026-06-08T08:34:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=834984)
[2026-06-08T08:34:25] Finding fusions and counting supporting reads (total=597730)
[2026-06-08T08:34:41] Merging adjacent fusion breakpoints (remaining=590952)
[2026-06-08T08:34:43] Filtering multi-mapping fusions by alignment score and read support (remaining=367827)
[2026-06-08T08:35:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=366064)
[2026-06-08T08:35:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=216246)
[2026-06-08T08:35:21] Filtering fusions with <2 supporting reads (remaining=30632)
[2026-06-08T08:35:22] Filtering fusions with an e-value >=0.3 (remaining=7652)
[2026-06-08T08:35:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7715)
[2026-06-08T08:35:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7614)
[2026-06-08T08:35:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7614)
[2026-06-08T08:35:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6971)
[2026-06-08T08:35:33] Searching for fusions with spliced split reads (remaining=6990)
[2026-06-08T08:35:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=4402)
[2026-06-08T08:35:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4372)
[2026-06-08T08:35:39] Searching for fusions with >=4 spliced events (remaining=5267)
[2026-06-08T08:35:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1937)
[2026-06-08T08:35:59] Filtering fusions with anchors <=23nt (remaining=1593)
[2026-06-08T08:36:00] Filtering end-to-end fusions with low support (remaining=1554)
[2026-06-08T08:36:00] Filtering fusions with no coverage around the breakpoints (remaining=1526)
[2026-06-08T08:36:01] Indexing gene sequences 
[2026-06-08T08:36:08] Filtering genes with >=30% identity (remaining=478)
[2026-06-08T08:36:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=247)
[2026-06-08T08:36:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=197)
[2026-06-08T08:36:16] Searching for additional isoforms (remaining=301)
[2026-06-08T08:36:17] Assigning confidence scores to events 
[2026-06-08T08:36:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:20] Writing fusions to file 'tih_rna_sample_00637_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:36:23] Writing discarded fusions to file 'tih_rna_sample_00637_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:51] Freeing resources
[2026-06-08T08:37:19] Done (elapsed time=00:11:51, CPU time=00:11:50, peak memory=15.3gb)