xargs: cat: terminated by signal 13

[namdeka]

Hi, I tried to run the command kraken2-build --db krakendb --build but this is the output I get:

I tried to change the treads and still ran into this issue. Could you tell me what is the problem?

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)... Estimated hash table requirement: 77039517988 bytes Capacity estimation complete. [53m36.403s] Building database files (step 3)... Taxonomy parsed and converted. xargs: cat: terminated by signal 13 /cvmfs/soft.ccr.buffalo.edu/versions/2023.01/easybuild/software/avx512/MPI/gcc/11.2.0/openmpi/4.1.1/kraken2/2.1.2/bin/build_kraken2_db.sh: line 143: 1538459 Done list_sequence_files 1538460 Exit 125 | xargs -0 cat 1538461 Killed | build_db -k $KRAKEN2_KMER_LEN -l $KRAKEN2_MINIMIZER_LEN -S $KRAKEN2_SEED_TEMPLATE $KRAKEN2XFLAG -H hash.k2d.tmp -t taxo.k2d.tmp -o opts.k2d.tmp -n taxonomy/ -m $seqid2taxid_map_file -c $required_capacity -p $KRAKEN2_THREAD_CT $max_db_flag -B $KRAKEN2_BLOCK_SIZE -b $KRAKEN2_SUBBLOCK_SIZE -r $KRAKEN2_MIN_TAXID_BITS $fast_build_flag

[B1991ing]

same issue

kraken2-build --db bacarcDB --build --threads 64

[gabridinosauro]

Hello I have the same. issue running it with this command: kraken2-build --build --db /xdisk/pkiela/schiro/petrullo/new_krak_db --threads 48

Thanks in advance, Gabri

[jenniferlu717]

@namdeka this normally happens if you do not have enough RAM for the database. In your case, you need 77Gb of RAM. What are the specs of your machine?

same for @B1991ing and @gabridinosauro

[gabridinosauro]

@jenniferlu717 Hi! Thanks for your reply. you are correct, I ended up giving more ram and it seems like it is working now. Maybe, just a suggestion, you could implelement an error message in the future that tells to give more ram if that error happens. Thanks again! Gabri