[2026-05-28T21:17:39] Launching Arriba 2.4.0
[2026-05-28T21:17:39] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:17:53] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:17:59] Reading chimeric alignments from 'LungN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=15581205)
[2026-05-28T21:26:30] Marking multi-mapping alignments (marked=11365387)
[2026-05-28T21:26:41] Detecting strandedness (reverse)
[2026-05-28T21:26:41] Assigning strands to alignments 
[2026-05-28T21:26:47] Annotating alignments 
[2026-05-28T21:27:44] Filtering duplicates (remaining=4783564)
[2026-05-28T21:27:52] 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=4087049)
[2026-05-28T21:27:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4087049)
[2026-05-28T21:27:59] Filtering viral contigs with expression lower than the top 5 (remaining=4087049)
[2026-05-28T21:28:07] Filtering viral contigs with less than 5% coverage (remaining=4087049)
[2026-05-28T21:28:10] Estimating fragment length (mate gap mean=-78.3525, mate gap stddev=29.9387, read length mean=114.789)
[2026-05-28T21:28:11] Filtering read-through fragments with a distance <=10000bp (remaining=3967480)
[2026-05-28T21:28:14] Filtering inconsistently clipped mates (remaining=3871820)
[2026-05-28T21:28:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3556565)
[2026-05-28T21:28:23] Filtering fragments with small insert size (remaining=3554246)
[2026-05-28T21:28:26] Filtering alignments with long gaps (remaining=3554246)
[2026-05-28T21:28:29] Filtering fragments with both mates in the same gene (remaining=3552763)
[2026-05-28T21:28:32] Filtering fusions arising from hairpin structures (remaining=3364004)
[2026-05-28T21:28:36] Filtering reads with a mismatch p-value <=0.01 (remaining=1184971)
[2026-05-28T21:28:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=380538)
[2026-05-28T21:28:57] Finding fusions and counting supporting reads (total=342824)
[2026-05-28T21:29:16] Merging adjacent fusion breakpoints (remaining=339929)
[2026-05-28T21:29:17] Filtering multi-mapping fusions by alignment score and read support (remaining=157437)
[2026-05-28T21:30:02] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:30:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=155443)
[2026-05-28T21:30:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=107604)
[2026-05-28T21:30:08] Filtering fusions with <2 supporting reads (remaining=5975)
[2026-05-28T21:30:09] Filtering fusions with an e-value >=0.3 (remaining=1499)
[2026-05-28T21:30:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1526)
[2026-05-28T21:30:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1395)
[2026-05-28T21:30:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1395)
[2026-05-28T21:30:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1359)
[2026-05-28T21:30:21] Searching for fusions with spliced split reads (remaining=1390)
[2026-05-28T21:30:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=1015)
[2026-05-28T21:30:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=991)
[2026-05-28T21:30:28] Searching for fusions with >=4 spliced events (remaining=1110)
[2026-05-28T21:30:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=384)
[2026-05-28T21:30:44] Filtering fusions with anchors <=23nt (remaining=323)
[2026-05-28T21:30:45] Filtering end-to-end fusions with low support (remaining=313)
[2026-05-28T21:30:46] Filtering fusions with no coverage around the breakpoints (remaining=309)
[2026-05-28T21:30:46] Indexing gene sequences 
[2026-05-28T21:30:48] Filtering genes with >=30% identity (remaining=98)
[2026-05-28T21:30:49] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=46)
[2026-05-28T21:30:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=43)
[2026-05-28T21:30:52] Searching for additional isoforms (remaining=48)
[2026-05-28T21:30:53] Assigning confidence scores to events 
[2026-05-28T21:30:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:30:56] Writing fusions to file 'LungN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:30:56] Writing discarded fusions to file 'LungN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:31:19] Freeing resources
[2026-05-28T21:31:43] Done (elapsed time=00:14:04, CPU time=00:14:03, peak memory=19.9gb)