Loading python/cpu/3.10.6 Loading requirement: tk/8.6.8 tcl/8.6.8 qt5/5.11.1 Generating chromosome sizes file... Processing sample: C6 Aligning with minimap2... [M::mm_idx_gen::72.367*1.52] collected minimizers [M::mm_idx_gen::90.849*1.91] sorted minimizers [M::main::90.849*1.91] loaded/built the index for 67 target sequence(s) [M::mm_mapopt_update::93.670*1.88] mid_occ = 597 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 67 [M::mm_idx_stat::95.257*1.86] distinct minimizers: 97776710 (39.85% are singletons); average occurrences: 5.139; average spacing: 5.435; total length: 2730876234 [M::worker_pipeline::287.202*8.71] mapped 1012471 sequences [M::worker_pipeline::451.821*11.56] mapped 1009991 sequences [M::worker_pipeline::575.992*13.24] mapped 1015118 sequences [M::worker_pipeline::684.440*14.49] mapped 1025701 sequences [M::worker_pipeline::783.080*15.39] mapped 1032676 sequences [M::worker_pipeline::896.916*16.07] mapped 1035454 sequences [M::worker_pipeline::1001.556*16.59] mapped 1022158 sequences [M::worker_pipeline::1109.381*17.07] mapped 1020173 sequences [M::worker_pipeline::1212.119*17.45] mapped 1027277 sequences [M::worker_pipeline::1320.175*17.81] mapped 1019959 sequences [M::worker_pipeline::1464.929*18.12] mapped 785873 sequences [M::worker_pipeline::1591.507*18.39] mapped 849609 sequences [M::worker_pipeline::1703.422*18.58] mapped 993324 sequences [M::worker_pipeline::1812.269*18.74] mapped 998005 sequences [M::worker_pipeline::1922.635*18.92] mapped 990085 sequences [M::worker_pipeline::2026.992*19.04] mapped 991011 sequences [M::worker_pipeline::2136.162*19.18] mapped 984900 sequences [M::worker_pipeline::2244.528*19.28] mapped 987583 sequences [M::worker_pipeline::2353.992*19.39] mapped 993830 sequences [M::worker_pipeline::2458.207*19.47] mapped 987473 sequences [M::worker_pipeline::2470.266*19.46] mapped 260616 sequences [M::main] Version: 2.28-r1209 [M::main] CMD: minimap2 -t 32 -ax map-ont /gpfs/data/boekelab/aleks/HOX_C6/HOXcombined.fa /gpfs/data/boekelab/aleks/HOX_C6/C6.fastq.gz [M::main] Real time: 2470.499 sec; CPU: 48071.129 sec; Peak RSS: 18.475 GB Sorting BAM... [bam_sort_core] merging from 0 files and 32 in-memory blocks... Indexing BAM... Generating bedGraph... Converting to bigWig... Running Sniffles2... 2025-06-13 12:25:11,138 INFO sniffles.main (3806386): Running Sniffles2, build 2.6.1 2025-06-13 12:25:11,138 INFO sniffles.main (3806386): Run Mode: call_sample 2025-06-13 12:25:11,138 INFO sniffles.main (3806386): Start on: 2025/06/13 12:25:11 2025-06-13 12:25:11,138 INFO sniffles.main (3806386): Working dir: /gpfs/data/boekelab/aleks/HOX_C6 2025-06-13 12:25:11,138 INFO sniffles.main (3806386): Used command: /gpfs/home/wudzia01/.local/bin/sniffles --input /gpfs/data/boekelab/aleks/HOX_C6/C6.sorted.bam --vcf /gpfs/data/boekelab/aleks/HOX_C6/C6_sniffles.vcf --reference /gpfs/data/boekelab/aleks/HOX_C6/HOXcombined.fa --threads 8 --minsupport 3 2025-06-13 12:25:11,138 INFO sniffles.main (3806386): ============================== 2025-06-13 12:25:11,412 INFO sniffles.main (3806386): Opening for reading: /gpfs/data/boekelab/aleks/HOX_C6/C6.sorted.bam 2025-06-13 12:25:11,434 INFO sniffles.main (3806386): Opening for reading: /gpfs/data/boekelab/aleks/HOX_C6/HOXcombined.fa 2025-06-13 12:25:11,477 INFO sniffles.main (3806386): Opening for writing: /gpfs/data/boekelab/aleks/HOX_C6/C6_sniffles.vcf (single-sample, sorted) 2025-06-13 12:25:11,520 INFO sniffles.main (3806386): 2025-06-13 12:25:11,520 INFO sniffles.main (3806386): Analyzing 31719123 alignments total... 2025-06-13 12:25:11,521 INFO sniffles.main (3806386): 2025-06-13 12:25:11,521 INFO sniffles.worker (3806386): Starting worker 0 2025-06-13 12:25:11,534 INFO sniffles.worker (3806386): Starting worker 1 2025-06-13 12:25:11,537 INFO sniffles.worker (3806386): Starting worker 2 2025-06-13 12:25:11,539 INFO sniffles.worker (3806386): Starting worker 3 2025-06-13 12:25:11,542 INFO sniffles.worker (3806386): Starting worker 4 2025-06-13 12:25:11,547 INFO sniffles.worker (3806386): Starting worker 5 2025-06-13 12:25:11,549 INFO sniffles.worker (3806386): Starting worker 6 2025-06-13 12:25:11,552 INFO sniffles.worker (3806386): Starting worker 7 2025-06-13 12:25:11,556 INFO sniffles.worker (3806386): Dispatched task #0 to worker 0 (66 tasks left) 2025-06-13 12:25:11,556 INFO sniffles.worker (3806386): Dispatched task #1 to worker 1 (65 tasks left) 2025-06-13 12:25:11,556 INFO sniffles.worker (3806386): Dispatched task #2 to worker 2 (64 tasks left) 2025-06-13 12:25:11,556 INFO sniffles.worker (3806386): Dispatched task #3 to worker 3 (63 tasks left) 2025-06-13 12:25:11,557 INFO sniffles.worker (3806386): Dispatched task #4 to worker 4 (62 tasks left) 2025-06-13 12:25:11,557 INFO sniffles.worker (3806386): Dispatched task #5 to worker 5 (61 tasks left) 2025-06-13 12:25:11,557 INFO sniffles.worker (3806386): Dispatched task #6 to worker 6 (60 tasks left) 2025-06-13 12:25:11,557 INFO sniffles.worker (3806386): Dispatched task #7 to worker 7 (59 tasks left) 2025-06-13 12:25:11,658 INFO sniffles.worker (3806386): Worker 0 got result for task #0 2025-06-13 12:25:11,830 INFO sniffles.worker (3806386): Dispatched task #8 to worker 0 (58 tasks left) 2025-06-13 12:25:26,226 INFO sniffles.worker (3806386): Worker 3 got result for task #3 2025-06-13 12:25:26,398 INFO sniffles.worker (3806386): Dispatched task #9 to worker 3 (57 tasks left) 2025-06-13 12:25:26,540 INFO sniffles.worker (3806386): Worker 0 got result for task #8 2025-06-13 12:25:26,602 INFO sniffles.worker (3806386): Worker 7 got result for task #7 2025-06-13 12:25:26,702 INFO sniffles.worker (3806386): Dispatched task #10 to worker 0 (56 tasks left) 2025-06-13 12:25:26,764 INFO sniffles.worker (3806386): Dispatched task #11 to worker 7 (55 tasks left) 2025-06-13 12:25:27,452 INFO sniffles.worker (3806386): Worker 4 got result for task #4 2025-06-13 12:25:27,624 INFO sniffles.worker (3806386): Dispatched task #12 to worker 4 (54 tasks left) 2025-06-13 12:25:27,624 INFO sniffles.worker (3806386): Worker 5 got result for task #5 2025-06-13 12:25:27,786 INFO sniffles.worker (3806386): Worker 4 got result for task #12 2025-06-13 12:25:27,786 INFO sniffles.worker (3806386): Dispatched task #13 to worker 5 (53 tasks left) 2025-06-13 12:25:27,787 INFO sniffles.worker (3806386): Worker 6 got result for task #6 2025-06-13 12:25:27,938 INFO sniffles.worker (3806386): Dispatched task #14 to worker 4 (52 tasks left) 2025-06-13 12:25:27,939 INFO sniffles.worker (3806386): Worker 5 got result for task #13 2025-06-13 12:25:27,939 INFO sniffles.worker (3806386): Dispatched task #15 to worker 6 (51 tasks left) 2025-06-13 12:25:28,090 INFO sniffles.worker (3806386): Worker 4 got result for task #14 2025-06-13 12:25:28,091 INFO sniffles.worker (3806386): Dispatched task #16 to worker 5 (50 tasks left) 2025-06-13 12:25:28,091 INFO sniffles.worker (3806386): Worker 6 got result for task #15 2025-06-13 12:25:28,243 INFO sniffles.worker (3806386): Dispatched task #17 to worker 4 (49 tasks left) 2025-06-13 12:25:28,243 INFO sniffles.worker (3806386): Worker 5 got result for task #16 2025-06-13 12:25:28,244 INFO sniffles.worker (3806386): Dispatched task #18 to worker 6 (48 tasks left) 2025-06-13 12:25:28,405 INFO sniffles.worker (3806386): Dispatched task #19 to worker 5 (47 tasks left) 2025-06-13 12:25:28,733 INFO sniffles.worker (3806386): Worker 2 got result for task #2 2025-06-13 12:25:28,905 INFO sniffles.worker (3806386): Dispatched task #20 to worker 2 (46 tasks left) 2025-06-13 12:25:29,076 INFO sniffles.worker (3806386): Worker 2 got result for task #20 2025-06-13 12:25:29,248 INFO sniffles.worker (3806386): Dispatched task #21 to worker 2 (45 tasks left) 2025-06-13 12:25:29,419 INFO sniffles.worker (3806386): Worker 2 got result for task #21 2025-06-13 12:25:29,591 INFO sniffles.worker (3806386): Dispatched task #22 to worker 2 (44 tasks left) 2025-06-13 12:25:29,763 INFO sniffles.worker (3806386): Worker 2 got result for task #22 2025-06-13 12:25:29,935 INFO sniffles.worker (3806386): Dispatched task #23 to worker 2 (43 tasks left) 2025-06-13 12:25:30,106 INFO sniffles.worker (3806386): Worker 2 got result for task #23 2025-06-13 12:25:30,278 INFO sniffles.worker (3806386): Dispatched task #24 to worker 2 (42 tasks left) 2025-06-13 12:25:30,450 INFO sniffles.worker (3806386): Worker 2 got result for task #24 2025-06-13 12:25:30,622 INFO sniffles.worker (3806386): Dispatched task #25 to worker 2 (41 tasks left) 2025-06-13 12:25:30,793 INFO sniffles.worker (3806386): Worker 2 got result for task #25 2025-06-13 12:25:30,965 INFO sniffles.worker (3806386): Dispatched task #26 to worker 2 (40 tasks left) 2025-06-13 12:25:32,401 INFO sniffles.worker (3806386): Worker 1 got result for task #1 2025-06-13 12:25:32,453 INFO sniffles.worker (3806386): Worker 7 got result for task #11 2025-06-13 12:25:32,564 INFO sniffles.worker (3806386): Dispatched task #27 to worker 1 (39 tasks left) 2025-06-13 12:25:32,616 INFO sniffles.worker (3806386): Dispatched task #28 to worker 7 (38 tasks left) 2025-06-13 12:25:32,727 INFO sniffles.worker (3806386): Worker 1 got result for task #27 2025-06-13 12:25:32,778 INFO sniffles.worker (3806386): Worker 7 got result for task #28 2025-06-13 12:25:32,889 INFO sniffles.worker (3806386): Dispatched task #29 to worker 1 (37 tasks left) 2025-06-13 12:25:32,941 INFO sniffles.worker (3806386): Dispatched task #30 to worker 7 (36 tasks left) 2025-06-13 12:25:33,052 INFO sniffles.worker (3806386): Worker 1 got result for task #29 2025-06-13 12:25:33,103 INFO sniffles.worker (3806386): Worker 7 got result for task #30 2025-06-13 12:25:33,214 INFO sniffles.worker (3806386): Dispatched task #31 to worker 1 (35 tasks left) 2025-06-13 12:25:33,266 INFO sniffles.worker (3806386): Dispatched task #32 to worker 7 (34 tasks left) 2025-06-13 12:25:33,376 INFO sniffles.worker (3806386): Worker 1 got result for task #31 2025-06-13 12:25:33,548 INFO sniffles.worker (3806386): Dispatched task #33 to worker 1 (33 tasks left) 2025-06-13 12:25:34,620 INFO sniffles.worker (3806386): Worker 0 got result for task #10 2025-06-13 12:25:34,792 INFO sniffles.worker (3806386): Dispatched task #34 to worker 0 (32 tasks left) 2025-06-13 12:25:34,964 INFO sniffles.worker (3806386): Worker 0 got result for task #34 2025-06-13 12:25:34,985 INFO sniffles.worker (3806386): Worker 3 got result for task #9 2025-06-13 12:25:35,127 INFO sniffles.worker (3806386): Dispatched task #35 to worker 0 (31 tasks left) 2025-06-13 12:25:35,148 INFO sniffles.worker (3806386): Dispatched task #36 to worker 3 (30 tasks left) 2025-06-13 12:25:40,990 INFO sniffles.worker (3806386): Worker 6 got result for task #18 2025-06-13 12:25:41,162 INFO sniffles.worker (3806386): Dispatched task #37 to worker 6 (29 tasks left) 2025-06-13 12:25:41,335 INFO sniffles.worker (3806386): Worker 6 got result for task #37 2025-06-13 12:25:41,507 INFO sniffles.worker (3806386): Dispatched task #38 to worker 6 (28 tasks left) 2025-06-13 12:25:41,669 INFO sniffles.worker (3806386): Worker 5 got result for task #19 2025-06-13 12:25:41,841 INFO sniffles.worker (3806386): Dispatched task #39 to worker 5 (27 tasks left) 2025-06-13 12:25:42,013 INFO sniffles.worker (3806386): Worker 5 got result for task #39 2025-06-13 12:25:42,185 INFO sniffles.worker (3806386): Dispatched task #40 to worker 5 (26 tasks left) 2025-06-13 12:25:43,782 INFO sniffles.worker (3806386): Worker 2 got result for task #26 2025-06-13 12:25:43,954 INFO sniffles.worker (3806386): Dispatched task #41 to worker 2 (25 tasks left) 2025-06-13 12:25:44,127 INFO sniffles.worker (3806386): Worker 2 got result for task #41 2025-06-13 12:25:44,299 INFO sniffles.worker (3806386): Dispatched task #42 to worker 2 (24 tasks left) 2025-06-13 12:25:44,471 INFO sniffles.worker (3806386): Worker 2 got result for task #42 2025-06-13 12:25:44,643 INFO sniffles.worker (3806386): Dispatched task #43 to worker 2 (23 tasks left) 2025-06-13 12:25:44,816 INFO sniffles.worker (3806386): Worker 2 got result for task #43 2025-06-13 12:25:44,988 INFO sniffles.worker (3806386): Dispatched task #44 to worker 2 (22 tasks left) 2025-06-13 12:25:45,160 INFO sniffles.worker (3806386): Worker 2 got result for task #44 2025-06-13 12:25:45,332 INFO sniffles.worker (3806386): Dispatched task #45 to worker 2 (21 tasks left) 2025-06-13 12:25:45,504 INFO sniffles.worker (3806386): Worker 2 got result for task #45 2025-06-13 12:25:45,676 INFO sniffles.worker (3806386): Dispatched task #46 to worker 2 (20 tasks left) 2025-06-13 12:25:45,718 INFO sniffles.worker (3806386): Worker 7 got result for task #32 2025-06-13 12:25:45,839 INFO sniffles.worker (3806386): Worker 2 got result for task #46 2025-06-13 12:25:45,880 INFO sniffles.worker (3806386): Dispatched task #47 to worker 7 (19 tasks left) 2025-06-13 12:25:45,981 INFO sniffles.worker (3806386): Worker 0 got result for task #35 2025-06-13 12:25:45,981 INFO sniffles.worker (3806386): Worker 1 got result for task #33 2025-06-13 12:25:45,982 INFO sniffles.worker (3806386): Dispatched task #48 to worker 2 (18 tasks left) 2025-06-13 12:25:46,023 INFO sniffles.worker (3806386): Worker 7 got result for task #47 2025-06-13 12:25:46,123 INFO sniffles.worker (3806386): Dispatched task #49 to worker 0 (17 tasks left) 2025-06-13 12:25:46,124 INFO sniffles.worker (3806386): Dispatched task #50 to worker 1 (16 tasks left) 2025-06-13 12:25:46,124 INFO sniffles.worker (3806386): Worker 2 got result for task #48 2025-06-13 12:25:46,165 INFO sniffles.worker (3806386): Dispatched task #51 to worker 7 (15 tasks left) 2025-06-13 12:25:46,266 INFO sniffles.worker (3806386): Worker 0 got result for task #49 2025-06-13 12:25:46,266 INFO sniffles.worker (3806386): Worker 1 got result for task #50 2025-06-13 12:25:46,266 INFO sniffles.worker (3806386): Dispatched task #52 to worker 2 (14 tasks left) 2025-06-13 12:25:46,307 INFO sniffles.worker (3806386): Worker 7 got result for task #51 2025-06-13 12:25:46,408 INFO sniffles.worker (3806386): Dispatched task #53 to worker 0 (13 tasks left) 2025-06-13 12:25:46,408 INFO sniffles.worker (3806386): Dispatched task #54 to worker 1 (12 tasks left) 2025-06-13 12:25:46,409 INFO sniffles.worker (3806386): Worker 2 got result for task #52 2025-06-13 12:25:46,450 INFO sniffles.worker (3806386): Dispatched task #55 to worker 7 (11 tasks left) 2025-06-13 12:25:46,550 INFO sniffles.worker (3806386): Worker 0 got result for task #53 2025-06-13 12:25:46,551 INFO sniffles.worker (3806386): Worker 1 got result for task #54 2025-06-13 12:25:46,551 INFO sniffles.worker (3806386): Dispatched task #56 to worker 2 (10 tasks left) 2025-06-13 12:25:46,592 INFO sniffles.worker (3806386): Worker 7 got result for task #55 2025-06-13 12:25:46,693 INFO sniffles.worker (3806386): Dispatched task #57 to worker 0 (9 tasks left) 2025-06-13 12:25:46,693 INFO sniffles.worker (3806386): Dispatched task #58 to worker 1 (8 tasks left) 2025-06-13 12:25:46,693 INFO sniffles.worker (3806386): Worker 2 got result for task #56 2025-06-13 12:25:46,735 INFO sniffles.worker (3806386): Dispatched task #59 to worker 7 (7 tasks left) 2025-06-13 12:25:46,835 INFO sniffles.worker (3806386): Worker 0 got result for task #57 2025-06-13 12:25:46,836 INFO sniffles.worker (3806386): Worker 1 got result for task #58 2025-06-13 12:25:46,836 INFO sniffles.worker (3806386): Dispatched task #60 to worker 2 (6 tasks left) 2025-06-13 12:25:46,877 INFO sniffles.worker (3806386): Worker 7 got result for task #59 2025-06-13 12:25:46,978 INFO sniffles.worker (3806386): Dispatched task #61 to worker 0 (5 tasks left) 2025-06-13 12:25:46,978 INFO sniffles.worker (3806386): Dispatched task #62 to worker 1 (4 tasks left) 2025-06-13 12:25:46,978 INFO sniffles.worker (3806386): Worker 2 got result for task #60 2025-06-13 12:25:47,020 INFO sniffles.worker (3806386): Dispatched task #63 to worker 7 (3 tasks left) 2025-06-13 12:25:47,120 INFO sniffles.worker (3806386): Worker 0 got result for task #61 2025-06-13 12:25:47,121 INFO sniffles.worker (3806386): Worker 1 got result for task #62 2025-06-13 12:25:47,121 INFO sniffles.worker (3806386): Dispatched task #64 to worker 2 (2 tasks left) 2025-06-13 12:25:47,162 INFO sniffles.worker (3806386): Worker 7 got result for task #63 2025-06-13 12:25:47,263 INFO sniffles.worker (3806386): Dispatched task #65 to worker 0 (1 tasks left) 2025-06-13 12:25:47,263 INFO sniffles.worker (3806386): Dispatched task #66 to worker 1 (0 tasks left) 2025-06-13 12:25:47,263 INFO sniffles.worker (3806386): Worker 2 got result for task #64 2025-06-13 12:25:47,304 INFO sniffles.worker (3806386): Worker 7 shutting down... 2025-06-13 12:25:47,405 INFO sniffles.worker (3806386): Worker 0 got result for task #65 2025-06-13 12:25:47,415 INFO sniffles.worker (3806386): Worker 2 shutting down... 2025-06-13 12:25:47,557 INFO sniffles.worker (3806386): Worker 0 shutting down... 2025-06-13 12:25:49,253 INFO sniffles.worker (3806386): Worker 5 got result for task #40 2025-06-13 12:25:49,394 INFO sniffles.worker (3806386): Worker 5 shutting down... 2025-06-13 12:25:49,395 INFO sniffles.worker (3806386): Worker 6 got result for task #38 2025-06-13 12:25:49,526 INFO sniffles.worker (3806386): Worker 6 shutting down... 2025-06-13 12:25:53,685 INFO sniffles.worker (3806386): Worker 1 got result for task #66 2025-06-13 12:25:53,806 INFO sniffles.worker (3806386): Worker 1 shutting down... 2025-06-13 12:25:54,782 INFO sniffles.worker (3806386): Worker 4 got result for task #17 2025-06-13 12:25:54,893 INFO sniffles.worker (3806386): Worker 4 shutting down... 2025-06-13 12:25:58,971 INFO sniffles.worker (3806386): Worker 3 got result for task #36 2025-06-13 12:25:59,072 INFO sniffles.worker (3806386): Worker 3 shutting down... 2025-06-13 12:25:59,072 INFO sniffles.worker (3806386): Worker 0 done (code 0). 2025-06-13 12:25:59,072 INFO sniffles.worker (3806386): Worker 1 done (code 0). 2025-06-13 12:25:59,072 INFO sniffles.worker (3806386): Worker 2 done (code 0). 2025-06-13 12:25:59,080 INFO sniffles.worker (3806386): Worker 3 done (code 0). 2025-06-13 12:25:59,080 INFO sniffles.worker (3806386): Worker 4 done (code 0). 2025-06-13 12:25:59,080 INFO sniffles.worker (3806386): Worker 5 done (code 0). 2025-06-13 12:25:59,080 INFO sniffles.worker (3806386): Worker 6 done (code 0). 2025-06-13 12:25:59,080 INFO sniffles.worker (3806386): Worker 7 done (code 0). 2025-06-13 12:25:59,080 INFO sniffles.main (3806386): Took 47.56s. 2025-06-13 12:25:59,080 INFO sniffles.main (3806386): 2025-06-13 12:26:00,219 INFO sniffles.main (3806386): Wrote 288 called SVs to /gpfs/data/boekelab/aleks/HOX_C6/C6_sniffles.vcf (single-sample, sorted) Finished processing C6 at Fri Jun 13 12:26:00 EDT 2025 Pipeline completed for all FASTQ files.