empty Reportfile #143
Comments
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2023-06-11T06:03:41.766209+02:00 linux systemd[1]: fwupd.service: Deactivated successfully. |
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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 |
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if you install kraken after krakenuniq you get a false classify file, you must install krakenuniq at last ! |
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Doesn't work even you install new ! :( and you define TMP :( with 128GB RAM + 150GB Swap :( and preload-size 40G |
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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 ! :( |
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Both Kraken2 and Krakenuniq are using classify but in different Versions ! 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. |
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 .
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