[2026-06-08T08:42:37] Launching Arriba 2.4.0
[2026-06-08T08:42:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:54] Reading chimeric alignments from 'tih_rna_sample_00701_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11100880)
[2026-06-08T08:50:54] Marking multi-mapping alignments (marked=7030897)
[2026-06-08T08:50:58] Detecting strandedness (reverse)
[2026-06-08T08:50:58] Assigning strands to alignments 
[2026-06-08T08:51:00] Annotating alignments 
[2026-06-08T08:51:31] Filtering duplicates (remaining=7536843)
[2026-06-08T08:51:38] 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=7261956)
[2026-06-08T08:51:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7261956)
[2026-06-08T08:51:42] Filtering viral contigs with expression lower than the top 5 (remaining=7261956)
[2026-06-08T08:51:47] Filtering viral contigs with less than 5% coverage (remaining=7261956)
[2026-06-08T08:51:50] Estimating fragment length (mate gap mean=-86.9462, mate gap stddev=30.3553, read length mean=138.172)
[2026-06-08T08:51:50] Filtering read-through fragments with a distance <=10000bp (remaining=6734472)
[2026-06-08T08:51:52] Filtering inconsistently clipped mates (remaining=6645415)
[2026-06-08T08:51:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6496974)
[2026-06-08T08:51:59] Filtering fragments with small insert size (remaining=6496505)
[2026-06-08T08:52:01] Filtering alignments with long gaps (remaining=6496505)
[2026-06-08T08:52:03] Filtering fragments with both mates in the same gene (remaining=6495382)
[2026-06-08T08:52:05] Filtering fusions arising from hairpin structures (remaining=6112658)
[2026-06-08T08:52:07] Filtering reads with a mismatch p-value <=0.01 (remaining=3203108)
[2026-06-08T08:52:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=1206739)
[2026-06-08T08:52:35] Finding fusions and counting supporting reads (total=833744)
[2026-06-08T08:52:51] Merging adjacent fusion breakpoints (remaining=824348)
[2026-06-08T08:52:53] Filtering multi-mapping fusions by alignment score and read support (remaining=530228)
[2026-06-08T08:53:25] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=527781)
[2026-06-08T08:53:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=280327)
[2026-06-08T08:53:34] Filtering fusions with <2 supporting reads (remaining=42054)
[2026-06-08T08:53:34] Filtering fusions with an e-value >=0.3 (remaining=14135)
[2026-06-08T08:53:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14191)
[2026-06-08T08:53:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14070)
[2026-06-08T08:53:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14070)
[2026-06-08T08:53:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10150)
[2026-06-08T08:53:46] Searching for fusions with spliced split reads (remaining=10291)
[2026-06-08T08:53:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=5497)
[2026-06-08T08:53:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5439)
[2026-06-08T08:53:54] Searching for fusions with >=4 spliced events (remaining=6520)
[2026-06-08T08:53:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2380)
[2026-06-08T08:54:12] Filtering fusions with anchors <=23nt (remaining=1844)
[2026-06-08T08:54:13] Filtering end-to-end fusions with low support (remaining=1788)
[2026-06-08T08:54:13] Filtering fusions with no coverage around the breakpoints (remaining=1731)
[2026-06-08T08:54:14] Indexing gene sequences 
[2026-06-08T08:54:21] Filtering genes with >=30% identity (remaining=575)
[2026-06-08T08:54:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=251)
[2026-06-08T08:54:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=216)
[2026-06-08T08:54:29] Searching for additional isoforms (remaining=282)
[2026-06-08T08:54:30] Assigning confidence scores to events 
[2026-06-08T08:54:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:33] Writing fusions to file 'tih_rna_sample_00701_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:54:36] Writing discarded fusions to file 'tih_rna_sample_00701_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:03] Freeing resources
[2026-06-08T08:55:20] Done (elapsed time=00:12:43, CPU time=00:12:43, peak memory=15.7gb)