jenniferlu717 / Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
http://ccb.jhu.edu/software/bracken/index.shtml
GNU General Public License v3.0
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Segmentation fault when trying to build krakenuniq database #262

Open jalalsiddiqui opened 7 months ago

jalalsiddiqui commented 7 months ago

I always have a segmentation fault when trying to build a krakenuniq database into bracken.. Any help will be appreciated.

**(krakenuniq) [user@server bracken_testing]$ bracken-build -d krakenuniq_db/ -t 16 -k 31 -l 150 -x /path/to/ -y krakenuniq

Selected Options: kmer length = 31 read length = 150 database = krakenuniq_db/ threads = 16 kraken type = krakenuniq Checking for Valid Options... Creating database.kraken [if not found] database.kraken exists, skipping creation.... Finished creating database.kraken [in DB folder] Creating database150mers.kmer_distrib STEP 0: PARSING COMMAND LINE ARGUMENTS Taxonomy nodes file: krakenuniq_db/taxonomy/nodes.dmp Seqid file: krakenuniq_db/seqid2taxid.map Num Threads: 16 Kmer Length: 31 Read Length: 150 STEP 1: READING SEQID2TAXID MAP 15253 total sequences read STEP 2: READING NODES.DMP FILE 2570190 total nodes read STEP 3: CONVERTING KMER MAPPINGS INTO READ CLASSIFICATIONS: 150mers, with a database built using 31mers 5 sequences converted (finished: M35256.1)11

/path/to//bracken-build: line 213: 211396 Segmentation fault (core dumped) kmer2read_distr --seqid2taxid $DATABASE/seqid2taxid.map --taxonomy $DATABASE/taxonomy/ --kraken $DATABASE/database.kraken --output $DATABASE/database${READ_LEN}mers.kraken -k ${KMER_LEN} -l ${READ_LEN} -t ${THREADS} (krakenuniq) [user@server bracken_testing]$**