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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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bracken 2.9 build error #253

Open 0russ4 opened 3 months ago

0russ4 commented 3 months ago

Hellow,I followed the correct procedure to build a standard database using Kraken2. However, when running bracken-build, I encountered the following error:

Selected Options: kmer length = 35 read length = 100 database = /public/home/hpc228111180/KRAKEN_DB2 threads = 1 kraken type = kraken2 Checking for Valid Options... Creating database.kraken [if not found] database.kraken exists, skipping creation.... Finished creating database.kraken [in DB folder] Creating database100mers.kmer_distrib STEP 0: PARSING COMMAND LINE ARGUMENTS Taxonomy nodes file: /public/home/hpc228111180/KRAKEN_DB2/taxonomy/nodes.dmp Seqid file: /public/home/hpc228111180/KRAKEN_DB2/seqid2taxid.map Num Threads: 1 Kmer Length: 35 Read Length: 100 STEP 1: READING SEQID2TAXID MAP 122373 total sequences read STEP 2: READING NODES.DMP FILE 2570096 total nodes read STEP 3: CONVERTING KMER MAPPINGS INTO READ CLASSIFICATIONS: 100mers, with a database built using 35mers 0 sequences converted...1 Bracken-2.9/bracken-build: 行 213: 191805 段错误 $DIR/src/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}

This issue has been troubling me for a long time. I have also tried running the code in segments, but it always fails at this part. Can you help me please?

ulin27 commented 3 months ago

Hi, I am also experiencing the same issue in step 3 (CONVERTING KMER MAPPINGS INTO READ CLASSIFICATIONS), resulting in a "segmentation fault (core dumped)" error. When I'm running the script, I specify to use the "largemem" partition on SLURM in addition to mem=0 (access to all memory on the node), but that doesn't seem to help. I've been struggling with Kraken2 and Bracken for weeks and am running out of time to solve this issue, as I'm set to defend my thesis very soon. Is there any way you can help with this? Thank you in advance!

Kaitlin

jenniferlu717 commented 1 month ago

@0russ4 im not 100% on what the issue is unfortunately. I dont see the error message. But if youre just building a standard database, the Bracken files and prebuild database is available at https://benlangmead.github.io/aws-indexes/k2

@ulin27 what database are you working with (and what database size?)