<![CDATA[KrakenUniq建库日志记录]]>Found jellyfish v1.1.12 Kraken build set to minimize disk writes. Found 12 sequence files (*.{fna,fa,ffn,fasta,fsa}) in the library directory. Skipping step 1, k-mer set already exists. Skipping step 2, no database reduction requested. Skipping step 3, k-mer set already sorted. Skipping step 4, seqID to taxID map already complete. Skipping step 5, taxDB exists. Skipping step 6, LCAs already set. Creating database summary report database.report.tsv ... /cromwell-executions/data/public_data/mngs/miniconda3/envs/tax_classifier/libexec/classify -d ././database.kdb -i ././database.idx -t 64 -r database.report.tsv -a ././taxDB -p 12 /dev/fd/63 Database ././database.kdb Loaded database with 43336394260 keys with k of 31 [val_len 4, key_len 8]. Reading taxonomy index from ././taxDB. Done. 25206200 sequences (291385.34 Mbp) processed in 27595.988s (54.8 Kseq/m, 633.54 Mbp/m). 25150113 sequences classified (99.78%) 56087 sequences unclassified (0.22%) Writing report file to database.report.tsv .. Reading genome sizes from ././database.kdb.counts ... done Setting values in the taxonomy tree ... done Printing classification report ... done Report finished in 90019.930 seconds. Finishing up ...Database construction complete. [Total: 32h51m9.712s] You can delete all files but database.{kdb,idx} and taxDB now, if you want ]]>http://an.forum.genostack.com/topic/282/krakenuniq建库日志记录RSS for NodeSat, 13 Jun 2026 09:36:43 GMTMon, 12 Apr 2021 09:46:26 GMT60<![CDATA[Reply to KrakenUniq建库日志记录 on Tue, 13 Apr 2021 01:28:27 GMT]]>@ice-melt

问题：xargs: cat: terminated by signal 13

Found jellyfish v1.1.12
Kraken build set to minimize disk writes.
Finding all library files
Found 12 sequence files (*.{fna,fa,ffn,fasta,fsa}) in the library directory.
Creating k-mer set (step 1 of 6)...
Using jellyfish
Hash size not specified, using '343468319717'
/cromwell-executions/data/public_data/mngs/miniconda3/envs/tax_classifier/libexec/build_db.sh: line 46: 42974 Killed                  jellyfish count -m 31 -s 343468319717 -C -t 10 -o database /dev/fd/63
xargs: cat: terminated by signal 13

内存不够时需要指定 --jellyfish-hash-size 20000M

]]>http://an.forum.genostack.com/post/582http://an.forum.genostack.com/post/582Tue, 13 Apr 2021 01:28:27 GMT