Building of standard database stops due to segmentation fault/broken pipe while "Setting LCAs in database (step 6 of 6)"

[flopezo]

Hello,

I'm trying to build the standard database using Kraken v1.0, but it stops during step 6:

Setting LCAs in database (step 6 of 6)... xargs: cat: terminated by signal 13 build_kraken_db.sh: line 204: 28665 Done find library/ '(' -name '*.fna' -o -name '*.fa' -o -name '*.ffn' ')' -print0 28666 Exit 125 | xargs -0 cat 28667 Segmentation fault | set_lcas $MEMFLAG -x -d database.kdb -i database.idx -n taxonomy/nodes.dmp -t $KRAKEN_THREAD_CT -m seqid2taxid.map -F /dev/fd/0

Any help would be greatly appreciated.

[jenniferlu717]

What command line did you use?

[flopezo]

I used kraken-build --threads 16 --standard --db /path/to/db

Thank you!

[flopezo]

I was able to successfully build a database using only the archaea and viral genomic libraries. However, when I added the library for bacteria (kraken-build --download-library bacteria), the database building process failed again during step 6 due to a segmentation fault.

[jenniferlu717]

There may just be some non-fasta file in your bacteria library folder that is causing this issue but I don't know exactly why this is happening. I was able to build the standard database myself without errors multiple times....

[jenniferlu717]

Hi, I was talking to someone else that works also on kraken databases and he suggested that the segmentation fault might just be due to the RAM usage of the database but we don't quite have a solution for it. I'm going to talk to Derrick Wood to see if there is some other solution.

[flopezo]

Thank you for your help, Jennifer.

[pvishwa2]

What was the solution to this issue? I'm still facing this problem, but haven't had any luck finishing the build using the solutions listed (upping RAM, re-downloading library).

[jenniferlu717]

I apologize, but we are no longer supporting kraken 1. Please use kraken 2: http://ccb.jhu.edu/software/kraken2/index.shtml

[feifeiyang123]

Hi, I had a same error when build standard database: Kraken build set to minimize disk writes. Creating k-mer set (step 1 of 6)... Found jellyfish v1.1.10 xargs: cat: terminated by signal 13

How can I fit it? Please help me!

[jkin2003]

same error output different step: Step 2/2: Assigning taxonomic IDs to sequences All files processed, cleaning up extra sequence files... done, library complete. Downloading UniVec_Core data from server... done. Adding taxonomy ID of 28384 to all sequences... done. Masking low-complexity regions of downloaded library... done. Creating sequence ID to taxonomy ID map (step 1)... Sequence ID to taxonomy ID map already present, skipping map creation. Estimating required capacity (step 2)... /work/k/kinskeyj/KrakenDownload/kraken2/scripts/build_kraken2_db.sh: line 101: estimate_capacity: command not found xargs: cat: terminated by signal 1