empty Reportfile

[JochenSchaefergmxde]

krakenuniq -db /mnt/m2/kuniqdb/kuniq_standard_plus_eupath_minus_kdb --threads 32 --exact --output /mnt/sdc1/rz/2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_O.txt --report-file /mnt/sdc1/rz/2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_R.txt /mnt/fastq/rz_TSAA8162_t2t_u_o.fastq.gz Warning: Overwriting /mnt/sdc1/rz/2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_R.txt. /usr/local/bin/classifyExact -d /mnt/m2/kuniqdb/kuniq_standard_plus_eupath_minus_kdb/database.kdb -i /mnt/m2/kuniqdb/kuniq_standard_plus_eupath_minus_kdb/database.idx -t 32 -o /mnt/sdc1/rz/2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_O.txt -r /mnt/sdc1/rz/2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_R.txt -a /mnt/m2/kuniqdb/kuniq_standard_plus_eupath_minus_kdb/taxDB -p 12 Database /mnt/m2/kuniqdb/kuniq_standard_plus_eupath_minus_kdb/database.kdb Loaded database with 34335766180 keys with k of 31 [val_len 4, key_len 8]. Reading taxonomy index from /mnt/m2/kuniqdb/kuniq_standard_plus_eupath_minus_kdb/taxDB. Done. Writing Kraken output to /mnt/sdc1/rz/2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_O.txt 59137302 sequences (7550.96 Mbp) processed in 3559.795s (996.8 Kseq/m, 127.27 Mbp/m). 58871764 sequences classified (99.55%) 265538 sequences unclassified (0.45%) Writing report file to /mnt/sdc1/rz/2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_R.txt .. Reading genome sizes from /mnt/m2/kuniqdb/kuniq_standard_plus_eupath_minus_kdb/database.kdb.counts ... done Setting values in the taxonomy tree ...(base)

Whats the Problem ??

cat /mnt/sdc1/rz/2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_R.txt

KrakenUniq v1.0.4 DATE:2023-05-28T09:36:43Z DB:/mnt/m2/kuniqdb/kuniq_standard_plus_eupath_minus_kdb DB_SIZE:412029195232 WD:/mnt/sdc1/rz/reports

CL:/usr/local/bin/krakenuniq -db /mnt/m2/kuniqdb/kuniq_standard_plus_eupath_minus_kdb --threads 32 --exact --output /mnt/sdc1/rz/2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_O.txt --report-file /mnt/sdc1/rz/2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_R.txt /mnt/fastq/rz_TSAA8162_t2t_u_o.fastq.gz

and nothing more, but in the Outputfile there are about 3792 Taxids listet. cut -f3 2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_O.txt|sort|uniq -c|sort -nr > 2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_O.csv

wc 2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_O.csv 3792 7584 56960 2023_05_28_10_24_10_rz_kuniq_stanTSAA8162t2tu_O.csv

So what could be wrong ? The System has a free -h gesamt benutzt frei gemns. Puffer/Cache verfügbar Speicher: 125Gi 2,0Gi 118Gi 64Mi 6,1Gi 123Gi Auslager: 136Gi 420Mi 136Gi

The Reportfile is also Null if i use the preload 8GB switch (--preload-size 8GB). !?

I try to convert the FastQ-File with fastp but nothing changed .

[JochenSchaefergmxde]

2023-06-11T06:03:41.766209+02:00 linux systemd[1]: fwupd.service: Deactivated successfully. 2023-06-11T06:08:54.189003+02:00 linux kernel: [66989.977652] classifyExact invoked oom-killer: gfp_mask=0x140cca(GFP_HIGHUSER_MOVABLE|GFP_COMP), order=0, oom_score_adj=0 2023-06-11T06:08:54.208257+02:00 linux kernel: [66989.977659] CPU: 23 PID: 6341 Comm: classifyExact Not tainted 6.2.0-20-generic #20-Ubuntu 2023-06-11T06:08:54.208259+02:00 linux kernel: [66989.977661] Hardware name: Gigabyte Technology Co., Ltd. Z790 GAMING X AX/Z790 GAMING X AX, BIOS F3k 01/05/2023 2023-06-11T06:08:54.208259+02:00 linux kernel: [66989.977662] Call Trace: 2023-06-11T06:08:54.208259+02:00 linux kernel: [66989.977664] 2023-06-11T06:08:54.208260+02:00 linux kernel: [66989.977666] dump_stack_lvl+0x48/0x70 2023-06-11T06:08:54.210425+02:00 linux kernel: [66989.977672] dump_stack+0x10/0x20 2023-06-11T06:08:54.210526+02:00 linux kernel: [66989.977674] dump_header+0x50/0x290 2023-06-11T06:08:54.210528+02:00 linux kernel: [66989.977677] oom_kill_process+0x10d/0x1c0 2023-06-11T06:08:54.210528+02:00 linux kernel: [66989.977678] out_of_memory+0x101/0x370 2023-06-11T06:08:54.210528+02:00 linux kernel: [66989.977679] __alloc_pages_may_oom+0x112/0x1e0 2023-06-11T06:08:54.210528+02:00 linux kernel: [66989.977682] alloc_pages_slowpath.constprop.0+0x4c7/0xa20 2023-06-11T06:08:54.210529+02:00 linux kernel: [66989.977684] alloc_pages+0x31d/0x350 2023-06-11T06:08:54.210529+02:00 linux kernel: [66989.977686] folio_alloc+0x1d/0x60 2023-06-11T06:08:54.210530+02:00 linux kernel: [66989.977687] ? policy_node+0x69/0x80 2023-06-11T06:08:54.210530+02:00 linux kernel: [66989.977690] vma_alloc_folio+0x9f/0x3d0 2023-06-11T06:08:54.210530+02:00 linux kernel: [66989.977691] read_swap_cache_async+0x119/0x290 2023-06-11T06:08:54.210530+02:00 linux kernel: [66989.977694] swap_cluster_readahead+0x250/0x3a0 2023-06-11T06:08:54.210530+02:00 linux kernel: [66989.977696] ? mod_memcg_lruvec_state+0x67/0x100 2023-06-11T06:08:54.212540+02:00 linux kernel: [66989.977698] swapin_readahead+0x45/0x80 2023-06-11T06:08:54.212547+02:00 linux kernel: [66989.977700] do_swap_page+0x185/0x930 2023-06-11T06:08:54.212547+02:00 linux kernel: [66989.977702] handle_pte_fault+0x202/0x240 2023-06-11T06:08:54.212547+02:00 linux kernel: [66989.977704] __handle_mm_fault+0x661/0x720 2023-06-11T06:08:54.212547+02:00 linux kernel: [66989.977706] handle_mm_fault+0x119/0x330 2023-06-11T06:08:54.212548+02:00 linux kernel: [66989.977708] do_user_addr_fault+0x1c1/0x720 2023-06-11T06:08:54.212550+02:00 linux kernel: [66989.977712] exc_page_fault+0x80/0x1b0 2023-06-11T06:08:54.212550+02:00 linux kernel: [66989.977714] asm_exc_page_fault+0x27/0x30 2023-06-11T06:08:54.212551+02:00 linux kernel: [66989.977717] RIP: 0033:0x7fcab9371330 2023-06-11T06:08:54.212551+02:00 linux kernel: [66989.977720] Code: c5 fe 6f 56 40 c5 fe 6f 5e 60 c5 fe 6f a6 00 10 00 00 c5 fe 6f ae 20 10 00 00 c5 fe 6f b6 40 10 00 00 c5 fe 6f be 60 10 00 00 7e 6f 86 00 20 00 00 c5 7e 6f 8e 20 20 00 00 c5 7e 6f 96 40 20 2023-06-11T06:08:54.212552+02:00 linux kernel: [66989.977721] RSP: 002b:00007f68c0d9bcf8 EFLAGS: 00010206 2023-06-11T06:08:54.212552+02:00 linux kernel: [66989.977723] RAX: 00007f2367fe6010 RBX: 00007f68c0d9bd60 RCX: 0000000000000020 2023-06-11T06:08:54.212552+02:00 linux kernel: [66989.977723] RDX: 0000000000003fd0 RSI: 00007f61c4e11040 RDI: 00007f25c4e02040 2023-06-11T06:08:54.212552+02:00 linux kernel: [66989.977724] RBP: 00007f68c0d9bd90 R08: ffffffffffffffd0 R09: 0000000000000000 2023-06-11T06:08:54.212552+02:00 linux kernel: [66989.977725] R10: 0000000000068c78 R11: 0000000001980000 R12: 0000000080000000 2023-06-11T06:08:54.212553+02:00 linux kernel: [66989.977726] R13: 00007f68842f1040 R14: 0000000400000000 R15: 00005634616a78e0 2023-06-11T06:08:54.212553+02:00 linux kernel: [66989.977728] 2023-06-11T06:08:54.212626+02:00 linux kernel: [66989.977729] Mem-Info: 2023-06-11T06:08:54.212631+02:00 linux kernel: [66989.977730] active_anon:711489 inactive_anon:31194802 isolated_anon:291 2023-06-11T06:08:54.212631+02:00 linux kernel: [66989.977730] active_file:1378 inactive_file:819 isolated_file:0 2023-06-11T06:08:54.212631+02:00 linux kernel: [66989.977730] unevictable:20280 dirty:0 writeback:57 2023-06-11T06:08:54.212632+02:00 linux kernel: [66989.977730] slab_reclaimable:373762 slab_unreclaimable:52201 2023-06-11T06:08:54.212632+02:00 linux kernel: [66989.977730] mapped:2042 shmem:17757 pagetables:335933 2023-06-11T06:08:54.212632+02:00 linux kernel: [66989.977730] sec_pagetables:0 bounce:0 2023-06-11T06:08:54.212632+02:00 linux kernel: [66989.977730] kernel_misc_reclaimable:0 2023-06-11T06:08:54.212633+02:00 linux kernel: [66989.977730] free:147488 free_pcp:0 free_cma:0 2023-06-11T06:08:54.212633+02:00 linux kernel: [66989.977733] Node 0 active_anon:2845956kB inactive_anon:124779208kB active_file:5512kB inactive_file:3276kB unevictable:81120kB isolated(anon):1164kB isolated(file):0kB mapped:8168kB dirty:0kB writeback:228kB shmem:71028kB shmem_thp: 47104kB shmem_pmdmapped: 0kB anon_thp: 0kB writeback_tmp:0kB kernel_stack:16544kB pagetables:1343732kB sec_pagetables:0kB all_unreclaimable? yes 2023-06-11T06:08:54.212635+02:00 linux kernel: [66989.977736] Node 0 DMA free:11264kB boost:0kB min:4kB low:16kB high:28kB reserved_highatomic:0KB active_anon:0kB inactive_anon:0kB active_file:0kB inactive_file:0kB unevictable:0kB writepending:0kB present:15992kB managed:15360kB mlocked:0kB bounce:0kB free_pcp:0kB local_pcp:0kB free_cma:0kB 2023-06-11T06:08:54.212768+02:00 linux kernel: [66989.977739] lowmem_reserve[]: 0 641 128466 128466 128466 2023-06-11T06:08:54.212774+02:00 linux kernel: [66989.977741] Node 0 DMA32 free:511636kB boost:0kB min:336kB low:992kB high:1648kB reserved_highatomic:0KB active_anon:2176kB inactive_anon:199764kB active_file:0kB inactive_file:24kB unevictable:856kB writepending:0kB present:798416kB managed:732516kB mlocked:0kB bounce:0kB free_pcp:0kB local_pcp:0kB free_cma:0kB

[JochenSchaefergmxde]

krakenuniq -db /mnt/m2/kuniqdb/kuniq_standard_plus_eupath_minus_kdb --threads 32 --exact --output /mnt/sdc1/rz/2023_06_11_11_53_54_rz_kuniq_stanTSAA8162t2tu_O.txt --preload-size 40GB --report-file /mnt/sdc1/rz/2023_06_11_11_53_54_rz_kuniq_stanTSAA8162t2tu_R.txt /mnt/fastq/rz_TSAA8162_t2t_u_o.fastq.gz

Even if i use preload-size 40GB (PC has 128GB) i get

2023-06-11T13:17:12.819421+02:00 linux kernel: [92687.959460] CPU: 19 PID: 9218 Comm: classifyExact Not tainted 6.2.0-20-generic #20-Ubuntu 2023-06-11T13:17:12.819427+02:00 linux kernel: [92687.959462] Hardware name: Gigabyte Technology Co., Ltd. Z790 GAMING X AX/Z790 GAMING X AX, BIOS F3k 01/05/2023 2023-06-11T13:17:12.819427+02:00 linux kernel: [92687.959463] Call Trace: 2023-06-11T13:17:12.819429+02:00 linux kernel: [92687.959464] 2023-06-11T13:17:12.819430+02:00 linux kernel: [92687.959466] dump_stack_lvl+0x48/0x70 2023-06-11T13:17:12.819430+02:00 linux kernel: [92687.959471] dump_stack+0x10/0x20 2023-06-11T13:17:12.819431+02:00 linux kernel: [92687.959473] dump_header+0x50/0x290 2023-06-11T13:17:12.819431+02:00 linux kernel: [92687.959476] oom_kill_process+0x10d/0x1c0 2023-06-11T13:17:12.819431+02:00 linux kernel: [92687.959477] out_of_memory+0x101/0x370 2023-06-11T13:17:12.819432+02:00 linux kernel: [92687.959479] alloc_pages_may_oom+0x112/0x1e0 2023-06-11T13:17:12.819432+02:00 linux kernel: [92687.959482] alloc_pages_slowpath.constprop.0+0x4c7/0xa20 2023-06-11T13:17:12.819432+02:00 linux kernel: [92687.959484] alloc_pages+0x31d/0x350 2023-06-11T13:17:12.819433+02:00 linux kernel: [92687.959486] folio_alloc+0x1d/0x60 2023-06-11T13:17:12.819433+02:00 linux kernel: [92687.959487] ? policy_node+0x69/0x80 2023-06-11T13:17:12.819433+02:00 linux kernel: [92687.959490] vma_alloc_folio+0x9f/0x3d0 2023-06-11T13:17:12.819434+02:00 linux kernel: [92687.959491] do_anonymous_page+0xfa/0x390 2023-06-11T13:17:12.819434+02:00 linux kernel: [92687.959494] handle_pte_fault+0x20f/0x240 2023-06-11T13:17:12.819435+02:00 linux kernel: [92687.959496] __handle_mm_fault+0x661/0x720 2023-06-11T13:17:12.819435+02:00 linux kernel: [92687.959498] handle_mm_fault+0x119/0x330 2023-06-11T13:17:12.819435+02:00 linux kernel: [92687.959500] do_user_addr_fault+0x1c1/0x720 2023-06-11T13:17:12.819435+02:00 linux kernel: [92687.959503] exc_page_fault+0x80/0x1b0 2023-06-11T13:17:12.819436+02:00 linux kernel: [92687.959506] asm_exc_page_fault+0x27/0x30 2023-06-11T13:17:12.819437+02:00 linux kernel: [92687.959509] RIP: 0033:0x7fbbda5713d7 2023-06-11T13:17:12.819438+02:00 linux kernel: [92687.959511] Code: 00 00 c5 7d e7 8f 20 20 00 00 c5 7d e7 97 40 20 00 00 c5 7d e7 9f 60 20 00 00 c5 7d e7 a7 00 30 00 00 c5 7d e7 af 20 30 00 00 7d e7 b7 40 30 00 00 c5 7d e7 bf 60 30 00 00 48 83 ef 80 ff c9 2023-06-11T13:17:12.819438+02:00 linux kernel: [92687.959512] RSP: 002b:00007f4fe3738cf8 EFLAGS: 00010203 2023-06-11T13:17:12.819438+02:00 linux kernel: [92687.959514] RAX: 00007f28e7fef010 RBX: 00007f4fe3738d60 RCX: 0000000000000001 2023-06-11T13:17:12.819439+02:00 linux kernel: [92687.959515] RDX: 0000000000003fd0 RSI: 00007f4a57064040 RDI: 00007f2c5705bfc0 2023-06-11T13:17:12.819439+02:00 linux kernel: [92687.959515] RBP: 00007f4fe3738d90 R08: ffffffffffffffd0 R09: 0000000000000000 2023-06-11T13:17:12.819439+02:00 linux kernel: [92687.959516] R10: 00000000000243e4 R11: 0000000001980000 R12: 0000000080000000 2023-06-11T13:17:12.819440+02:00 linux kernel: [92687.959517] R13: 000055d95dd6acd0 R14: 0000000400000000 R15: 000055d961354d60 2023-06-11T13:17:12.819440+02:00 linux kernel: [92687.959519] 2023-06-11T13:17:12.819441+02:00 linux kernel: [92687.959520] Mem-Info: 2023-06-11T13:17:12.819441+02:00 linux kernel: [92687.959521] active_anon:5382938 inactive_anon:26584760 isolated_anon:0 2023-06-11T13:17:12.819441+02:00 linux kernel: [92687.959521] active_file:529 inactive_file:1895 isolated_file:66 2023-06-11T13:17:12.819441+02:00 linux kernel: [92687.959521] unevictable:15757 dirty:0 writeback:0 2023-06-11T13:17:12.819442+02:00 linux kernel: [92687.959521] slab_reclaimable:316950 slab_unreclaimable:51095 2023-06-11T13:17:12.819442+02:00 linux kernel: [92687.959521] mapped:997 shmem:18568 pagetables:337704 2023-06-11T13:17:12.819442+02:00 linux kernel: [92687.959521] sec_pagetables:0 bounce:0 2023-06-11T13:17:12.819442+02:00 linux kernel: [92687.959521] kernel_misc_reclaimable:0 2023-06-11T13:17:12.819443+02:00 linux kernel: [92687.959521] free:147100 free_pcp:0 free_cma:0 2023-06-11T13:17:12.819443+02:00 linux kernel: [92687.959524] Node 0 active_anon:21531752kB inactive_anon:106339040kB active_file:2116kB inactive_file:7580kB unevictable:63028kB isolated(anon):0kB isolated(file):264kB mapped:3988kB dirty:0kB writeback:0kB shmem:74272kB shmem_thp: 45056kB shmem_pmdmapped: 0kB anon_thp: 0kB writeback_tmp:0kB kernel_stack:16576kB pagetables:1350816kB sec_pagetables:0kB all_unreclaimable? no

[JochenSchaefergmxde]

if you install kraken after krakenuniq you get a false classify file, you must install krakenuniq at last !

[JochenSchaefergmxde]

Doesn't work even you install new ! :( and you define TMP :( with 128GB RAM + 150GB Swap :( and preload-size 40G

[JochenSchaefergmxde]

It seems to be the "exact" switch how made the Problems !. If the fastq is about 2GB i get a memory Error in syslog with classifyexact. classify should work, this is called without "-exact" switch ! :(

[JochenSchaefergmxde]

Both Kraken2 and Krakenuniq are using classify but in different Versions ! software/krakenuniq/src/classify.cpp software/krakenuniq/src/classifyExact software/krakenuniq/src/classify software/kraken2/src/classify.cc software/kraken2/src/classify software/kraken2/src/classify.o

So you cant install it in the same place like /usr/local/bin .

If you want to use both you must install it in different locations and attention to you PATH variable.