krakenuniq --report-file res_archaea.tsv --db archaea_db --threads 10 test_archaea.fna

krakenuniq构建数据库参数说明

构建过程中需要6步，可以重复运行，每次运行会检查之前的文件确定是否需要运行当前步骤
不指定--jellyfish-hash-size会使用全部内存，内存不够会报错，建议根据服务器内存大小指定该参数

Usage: krakenuniq-build [task option] [options]

Task options (exactly one can be selected -- default is build):
  --download-taxonomy        Download NCBI taxonomic information
  --download-library TYPE    Download partial library (TYPE = one of "refseq/bacteria", "refseq/archaea", "refseq/viral"). 
                             Use krakenuniq-download for more options.
  --add-to-library FILE      Add FILE to library
  --build                    Create DB from library (requires taxonomy d/l'ed and at 
                             least one file in library)
  --rebuild                  Create DB from library like --build, but remove
                             existing non-library/taxonomy files before build
  --clean                    Remove unneeded files from a built database
  --shrink NEW_CT            Shrink an existing DB to have only NEW_CT k-mers
  --standard                 Download and create default database, which contains complete genomes 
                             for archaea, bacteria and viruses from RefSeq, as well as viral strains 
                             from NCBI. Specify --taxids-for-genomes and --taxids-for-sequences
                             separately, if desired.

  --help                     Print this message
  --version                  Print version information

Options:
  --db DBDIR                 Kraken DB directory (mandatory except for --help/--version)
  --threads #                Number of threads (def: 1)
  --new-db NAME              New Kraken DB name (shrink task only; mandatory
                             for shrink task)
  --kmer-len NUM             K-mer length in bp (build/shrink tasks only;
                             def: 31)
  --minimizer-len NUM        Minimizer length in bp (build/shrink tasks only;
                             def: 15)
  --jellyfish-hash-size STR  Pass a specific hash size argument to jellyfish
                             when building database (build task only)
  --jellyfish-bin STR        Use STR as Jellyfish 1 binary.
  --max-db-size SIZE         Shrink the DB before full build, making sure
                             database and index together use <= SIZE gigabytes
                             (build task only)
  --shrink-block-offset NUM  When shrinking, select the k-mer that is NUM
                             positions from the end of a block of k-mers
                             (default: 1)
  --work-on-disk             Perform most operations on disk rather than in
                             RAM (will slow down build in most cases)
  --taxids-for-genomes       Add taxonomy IDs (starting with 1 billion) for genomes.
                             Only works with 3-column seqid2taxid map with third 
                             column being the name
  --taxids-for-sequences     Add taxonomy IDs for sequences, starting with 1 billion.
                             Can be useful to resolve classifications with multiple genomes
                             for one taxonomy ID.
  --min-contig-size NUM      Minimum contig size for inclusion in database.
                             Use with draft genomes to reduce contamination, e.g. with values between 1000 and 10000.
  --library-dir DIR          Use DIR for reference sequences instead of DBDIR/library.
  --taxonomy-dir DIR         Use DIR for taxonomy instead of DBDIR/taxonomy.

Experimental:
  --uid-database             Build a UID database (default no)
  --lca-database             Build a LCA database (default yes)
  --no-lca-database          Do not build a LCA database
  --lca-order DIR1           Impose a hierarchical order for setting LCAs.
  --lca-order DIR2           The directories must be specified relative to the libary directory
  ...                        (DBDIR/library). When setting the LCAs, k-mers from sequences in
                             DIR1 will be set first, and only unset k-mers will be set from
                             DIR2, etc, and final from the whole library.
							 Use this option when including low-confidence draft genomes,
                             e.g use --lca-order Complete_Genome --lca-order Chromosome to
                             prioritize more complete assemblies.
                             Keep in mind that this option takes considerably longer.

使用krakenuniq分析数据命令参数说明

Usage: krakenuniq --report-file FILENAME [options] <filename(s)>

Options:
  --db NAME               Name for Kraken DB (default: none)
  --threads NUM           Number of threads (default: 1)
  --fasta-input           Input is FASTA format
  --fastq-input           Input is FASTQ format
  --gzip-compressed       Input is gzip compressed
  --bzip2-compressed      Input is bzip2 compressed
  --hll-precision INT     Precision for HyperLogLog k-mer cardinality estimation, between 10 and 18 (default: 12)
  --exact                 Compute exact cardinality instead of estimate (slower, requires memory proportional to cardinality!)
  --quick                 Quick operation (use first hit or hits)
  --min-hits NUM          In quick op., number of hits req'd for classification
                          NOTE: this is ignored if --quick is not specified
  --unclassified-out FILENAME
                          Print unclassified sequences to filename
  --classified-out FILENAME
                          Print classified sequences to filename
  --output FILENAME       Print output to filename (default: stdout); "off" will
                          suppress normal output
  --only-classified-output
                          Print no Kraken output for unclassified sequences
  --preload               Loads DB into memory before classification
  --paired                The two filenames provided are paired-end reads
  --check-names           Ensure each pair of reads have names that agree
                          with each other; ignored if --paired is not specified
  --help                  Print this message
  --version               Print version information

Experimental:
  --uid-mapping           Map using UID database

If none of the *-input or *-compressed flags are specified, and the 
file is a regular file, automatic format detection is attempted.

https://github.com/DerrickWood/kraken/issues/65

http://gensoft.pasteur.fr/docs/kraken/0.10.5-beta/MANUAL.html
http://gensoft.pasteur.fr/docs/kraken/0.10.5-beta/MANUAL.html

There is no current way to combine builds due to the way that the database is stored in memory.

目录中有一个nt.fna为370GB多 因此把library-files.txt删掉 重新build 试试 build 命令会自动找library目录下面的文件

如果library中的数据比较多 krakenuniq非常耗费内存 中间在jellyfish的步骤会被kill掉 因此需要一个一个的处理library中的数据 ，例如先处理细菌的 再处理病毒的 正常的打印如下：

krakenuniq-build --db . --kmer-len 31 --threads 15 --taxids-for-genomes --taxids-for-sequences --jellyfish-hash-size 5000M
Found jellyfish v1.1.11
Kraken build set to minimize disk writes.
Found 2 sequence files (*.{fna,fa,ffn,fasta,fsa}) in the library directory.
Creating k-mer set (step 1 of 6)...
Using jellyfish
K-mer set created. [2m30.142s]
Skipping step 2, no database reduction requested.
Sorting k-mer set (step 3 of 6)...
db_sort: Getting database into memory ...Loaded database with 801475581 keys with k of 31 [val_len 4, key_len 8].
Loaded database with 801475581 keys with k of 31 [val_len 4, key_len 8].
db_sort: Sorting ...db_sort: Sorting complete - writing database to disk ...
K-mer set sorted. [8m26.865s]
Creating seqID to taxID map (step 4 of 6)..
18949 sequences mapped to taxa. [0.023s]
Creating taxDB (step 5 of 6)...
Building taxonomy index from taxonomy//nodes.dmp and taxonomy//names.dmp. Done, got 2312242 taxa
taxDB construction finished. [11.991s]
Building KrakenUniq LCA database (step 6 of 6)...
Adding taxonomy IDs for sequences
Adding taxonomy IDs for genomes
Reading taxonomy index from taxDB. Done.
Getting database0.kdb into memory (8.957 GB) ... Done
Loaded database with 801475581 keys with k of 31 [val_len 4, key_len 8].
Reading sequence ID to taxonomy ID mapping ... [starting new taxonomy IDs with 1000000001] got 18949 mappings.
Finished processing 37898 sequences (skipping 0 empty sequences, and 0 sequences with no taxonomy mapping)
Writing kmer counts to database.kdb.counts...
Writing database from RAM back to database.kdb ...
Writing new TaxDB ...
LCA database created. [5m10.060s]
Creating database summary report database.report.tsv ...
/home/bioinfo/miniconda2/envs/tax_classifier/libexec/classify -d ././database.kdb -i ././database.idx -t 15 -r database.report.tsv -a ././taxDB -p 12 /dev/fd/63
Database ././database.kdb
Loaded database with 801475581 keys with k of 31 [val_len 4, key_len 8].
Reading taxonomy index from ././taxDB. Done.
37898 sequences (2276.87 Mbp) processed in 42.084s (54.0 Kseq/m, 3246.14 Mbp/m).
37869 sequences classified (99.92%)
29 sequences unclassified (0.08%)
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 0.247 seconds.
Finishing up ...Database construction complete. [Total: 17m6.972s]
You can delete all files but database.{kdb,idx} and taxDB now, if you want